{ "cells": [ { "cell_type": "markdown", "id": "c3f43948", "metadata": {}, "source": [ "# Length dependency of conformational change" ] }, { "cell_type": "markdown", "id": "23364e75", "metadata": {}, "source": [ "## Introduction\n", "\n", "In this notebook, we set out to determine if there was a correlation between conformational change and the length of CDR loops or peptides.\n", "We looked at both the correlation of bulk movements when loops where aligned on the framework regions and also the deformation effects when loops are aligned to one another.\n", "All peptide conformations are measure from alignment on the antigen binding groove floor." ] }, { "cell_type": "code", "execution_count": 1, "id": "765a694e", "metadata": {}, "outputs": [], "source": [ "import os\n", "\n", "import matplotlib.pyplot as plt\n", "import pandas as pd\n", "import numpy as np\n", "import scipy\n", "import seaborn as sns" ] }, { "cell_type": "markdown", "id": "a29a7531", "metadata": {}, "source": [ "## Loading Meta data" ] }, { "cell_type": "code", "execution_count": 2, "id": "08d3997f", "metadata": {}, "outputs": [], "source": [ "DATA_DIR = '../data/processed/apo-holo-tcr-pmhc-class-I-comparisons'" ] }, { "cell_type": "code", "execution_count": 3, "id": "ab6eb5e3", "metadata": {}, "outputs": [], "source": [ "apo_holo_summary_df = pd.read_csv('../data/processed/apo-holo-tcr-pmhc-class-I/apo_holo_summary.csv')\n", "\n", "apo_holo_summary_df['id'] = apo_holo_summary_df['file_name'].str.replace('.pdb$', '', regex=True)" ] }, { "cell_type": "code", "execution_count": 4, "id": "8d90718a", "metadata": {}, "outputs": [], "source": [ "cdr_types = ['CDR-A1', 'CDR-A2', 'CDR-A3','CDR-B1', 'CDR-B2', 'CDR-B3']\n", "apo_holo_summary_df[cdr_types] = apo_holo_summary_df['cdr_sequences_collated'].str.split('-').apply(pd.Series)" ] }, { "cell_type": "code", "execution_count": 5, "id": "244f1c48", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
\n", " | file_name | \n", "pdb_id | \n", "structure_type | \n", "state | \n", "alpha_chain | \n", "beta_chain | \n", "antigen_chain | \n", "mhc_chain1 | \n", "mhc_chain2 | \n", "cdr_sequences_collated | \n", "peptide_sequence | \n", "mhc_slug | \n", "id | \n", "CDR-A1 | \n", "CDR-A2 | \n", "CDR-A3 | \n", "CDR-B1 | \n", "CDR-B2 | \n", "CDR-B3 | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | \n", "1ao7_D-E-C-A-B_tcr_pmhc.pdb | \n", "1ao7 | \n", "tcr_pmhc | \n", "holo | \n", "D | \n", "E | \n", "C | \n", "A | \n", "B | \n", "DRGSQS-IYSNGD-AVTTDSWGKLQ-MNHEY-SVGAGI-ASRPGLA... | \n", "LLFGYPVYV | \n", "hla_a_02_01 | \n", "1ao7_D-E-C-A-B_tcr_pmhc | \n", "DRGSQS | \n", "IYSNGD | \n", "AVTTDSWGKLQ | \n", "MNHEY | \n", "SVGAGI | \n", "ASRPGLAGGRPEQY | \n", "
1 | \n", "1b0g_C-A-B_pmhc.pdb | \n", "1b0g | \n", "pmhc | \n", "apo | \n", "NaN | \n", "NaN | \n", "C | \n", "A | \n", "B | \n", "NaN | \n", "ALWGFFPVL | \n", "hla_a_02_01 | \n", "1b0g_C-A-B_pmhc | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
2 | \n", "1b0g_F-D-E_pmhc.pdb | \n", "1b0g | \n", "pmhc | \n", "apo | \n", "NaN | \n", "NaN | \n", "F | \n", "D | \n", "E | \n", "NaN | \n", "ALWGFFPVL | \n", "hla_a_02_01 | \n", "1b0g_F-D-E_pmhc | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
3 | \n", "1bd2_D-E-C-A-B_tcr_pmhc.pdb | \n", "1bd2 | \n", "tcr_pmhc | \n", "holo | \n", "D | \n", "E | \n", "C | \n", "A | \n", "B | \n", "NSMFDY-ISSIKDK-AAMEGAQKLV-MNHEY-SVGAGI-ASSYPGG... | \n", "LLFGYPVYV | \n", "hla_a_02_01 | \n", "1bd2_D-E-C-A-B_tcr_pmhc | \n", "NSMFDY | \n", "ISSIKDK | \n", "AAMEGAQKLV | \n", "MNHEY | \n", "SVGAGI | \n", "ASSYPGGGFYEQY | \n", "
4 | \n", "1bii_P-A-B_pmhc.pdb | \n", "1bii | \n", "pmhc | \n", "apo | \n", "NaN | \n", "NaN | \n", "P | \n", "A | \n", "B | \n", "NaN | \n", "RGPGRAFVTI | \n", "h2_dd | \n", "1bii_P-A-B_pmhc | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
386 | \n", "7rtd_C-A-B_pmhc.pdb | \n", "7rtd | \n", "pmhc | \n", "apo | \n", "NaN | \n", "NaN | \n", "C | \n", "A | \n", "B | \n", "NaN | \n", "YLQPRTFLL | \n", "hla_a_02_01 | \n", "7rtd_C-A-B_pmhc | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "NaN | \n", "
387 | \n", "7rtr_D-E-C-A-B_tcr_pmhc.pdb | \n", "7rtr | \n", "tcr_pmhc | \n", "holo | \n", "D | \n", "E | \n", "C | \n", "A | \n", "B | \n", "DRGSQS-IYSNGD-AVNRDDKII-SEHNR-FQNEAQ-ASSPDIEQY | \n", "YLQPRTFLL | \n", "hla_a_02_01 | \n", "7rtr_D-E-C-A-B_tcr_pmhc | \n", "DRGSQS | \n", "IYSNGD | \n", "AVNRDDKII | \n", "SEHNR | \n", "FQNEAQ | \n", "ASSPDIEQY | \n", "
388 | \n", "8gvb_A-B-P-H-L_tcr_pmhc.pdb | \n", "8gvb | \n", "tcr_pmhc | \n", "holo | \n", "A | \n", "B | \n", "P | \n", "H | \n", "L | \n", "YGATPY-YFSGDTLV-AVGFTGGGNKLT-SEHNR-FQNEAQ-ASSD... | \n", "RYPLTFGW | \n", "hla_a_24_02 | \n", "8gvb_A-B-P-H-L_tcr_pmhc | \n", "YGATPY | \n", "YFSGDTLV | \n", "AVGFTGGGNKLT | \n", "SEHNR | \n", "FQNEAQ | \n", "ASSDRDRVPETQY | \n", "
389 | \n", "8gvg_A-B-P-H-L_tcr_pmhc.pdb | \n", "8gvg | \n", "tcr_pmhc | \n", "holo | \n", "A | \n", "B | \n", "P | \n", "H | \n", "L | \n", "YGATPY-YFSGDTLV-AVGFTGGGNKLT-SEHNR-FQNEAQ-ASSD... | \n", "RFPLTFGW | \n", "hla_a_24_02 | \n", "8gvg_A-B-P-H-L_tcr_pmhc | \n", "YGATPY | \n", "YFSGDTLV | \n", "AVGFTGGGNKLT | \n", "SEHNR | \n", "FQNEAQ | \n", "ASSDRDRVPETQY | \n", "
390 | \n", "8gvi_A-B-P-H-L_tcr_pmhc.pdb | \n", "8gvi | \n", "tcr_pmhc | \n", "holo | \n", "A | \n", "B | \n", "P | \n", "H | \n", "L | \n", "YGATPY-YFSGDTLV-AVVFTGGGNKLT-SEHNR-FQNEAQ-ASSL... | \n", "RYPLTFGW | \n", "hla_a_24_02 | \n", "8gvi_A-B-P-H-L_tcr_pmhc | \n", "YGATPY | \n", "YFSGDTLV | \n", "AVVFTGGGNKLT | \n", "SEHNR | \n", "FQNEAQ | \n", "ASSLRDRVPETQY | \n", "
391 rows × 19 columns
\n", "\n", " | complex_id | \n", "structure_x_name | \n", "structure_y_name | \n", "chain_type | \n", "cdr | \n", "rmsd | \n", "alignment | \n", "
---|---|---|---|---|---|---|---|
0 | \n", "3qdg_D-E-C-A-B_tcr_pmhc | \n", "3qdg_D-E-C-A-B_tcr_pmhc.pdb | \n", "3qeu_A-B_tcr.pdb | \n", "alpha_chain | \n", "1 | \n", "1.932806 | \n", "framework | \n", "
1 | \n", "3qdg_D-E-C-A-B_tcr_pmhc | \n", "3qdg_D-E-C-A-B_tcr_pmhc.pdb | \n", "3qeu_A-B_tcr.pdb | \n", "alpha_chain | \n", "2 | \n", "1.308598 | \n", "framework | \n", "
2 | \n", "3qdg_D-E-C-A-B_tcr_pmhc | \n", "3qdg_D-E-C-A-B_tcr_pmhc.pdb | \n", "3qeu_A-B_tcr.pdb | \n", "alpha_chain | \n", "3 | \n", "1.244062 | \n", "framework | \n", "
3 | \n", "3qdg_D-E-C-A-B_tcr_pmhc | \n", "3qdg_D-E-C-A-B_tcr_pmhc.pdb | \n", "3qeu_A-B_tcr.pdb | \n", "beta_chain | \n", "1 | \n", "0.809066 | \n", "framework | \n", "
4 | \n", "3qdg_D-E-C-A-B_tcr_pmhc | \n", "3qdg_D-E-C-A-B_tcr_pmhc.pdb | \n", "3qeu_A-B_tcr.pdb | \n", "beta_chain | \n", "2 | \n", "0.688597 | \n", "framework | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
809 | \n", "7rtr_D-E-C-A-B_tcr_pmhc | \n", "7n1d_A-B_tcr.pdb | \n", "7rtr_D-E-C-A-B_tcr_pmhc.pdb | \n", "alpha_chain | \n", "2 | \n", "0.206414 | \n", "loop | \n", "
810 | \n", "7rtr_D-E-C-A-B_tcr_pmhc | \n", "7n1d_A-B_tcr.pdb | \n", "7rtr_D-E-C-A-B_tcr_pmhc.pdb | \n", "alpha_chain | \n", "3 | \n", "0.459090 | \n", "loop | \n", "
811 | \n", "7rtr_D-E-C-A-B_tcr_pmhc | \n", "7n1d_A-B_tcr.pdb | \n", "7rtr_D-E-C-A-B_tcr_pmhc.pdb | \n", "beta_chain | \n", "1 | \n", "0.255668 | \n", "loop | \n", "
812 | \n", "7rtr_D-E-C-A-B_tcr_pmhc | \n", "7n1d_A-B_tcr.pdb | \n", "7rtr_D-E-C-A-B_tcr_pmhc.pdb | \n", "beta_chain | \n", "2 | \n", "0.175123 | \n", "loop | \n", "
813 | \n", "7rtr_D-E-C-A-B_tcr_pmhc | \n", "7n1d_A-B_tcr.pdb | \n", "7rtr_D-E-C-A-B_tcr_pmhc.pdb | \n", "beta_chain | \n", "3 | \n", "0.223801 | \n", "loop | \n", "
1628 rows × 7 columns
\n", "\n", " | file_name | \n", "pdb_id | \n", "structure_type | \n", "state | \n", "alpha_chain | \n", "beta_chain | \n", "antigen_chain | \n", "mhc_chain1 | \n", "mhc_chain2 | \n", "cdr_sequences_collated | \n", "peptide_sequence | \n", "mhc_slug | \n", "id | \n", "cdr_type | \n", "cdr_sequence | \n", "chain_type | \n", "cdr | \n", "cdr_length | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | \n", "1ao7_D-E-C-A-B_tcr_pmhc.pdb | \n", "1ao7 | \n", "tcr_pmhc | \n", "holo | \n", "D | \n", "E | \n", "C | \n", "A | \n", "B | \n", "DRGSQS-IYSNGD-AVTTDSWGKLQ-MNHEY-SVGAGI-ASRPGLA... | \n", "LLFGYPVYV | \n", "hla_a_02_01 | \n", "1ao7_D-E-C-A-B_tcr_pmhc | \n", "CDR-A1 | \n", "DRGSQS | \n", "alpha_chain | \n", "1 | \n", "6.0 | \n", "
1 | \n", "1b0g_C-A-B_pmhc.pdb | \n", "1b0g | \n", "pmhc | \n", "apo | \n", "NaN | \n", "NaN | \n", "C | \n", "A | \n", "B | \n", "NaN | \n", "ALWGFFPVL | \n", "hla_a_02_01 | \n", "1b0g_C-A-B_pmhc | \n", "CDR-A1 | \n", "NaN | \n", "alpha_chain | \n", "1 | \n", "NaN | \n", "
2 | \n", "1b0g_F-D-E_pmhc.pdb | \n", "1b0g | \n", "pmhc | \n", "apo | \n", "NaN | \n", "NaN | \n", "F | \n", "D | \n", "E | \n", "NaN | \n", "ALWGFFPVL | \n", "hla_a_02_01 | \n", "1b0g_F-D-E_pmhc | \n", "CDR-A1 | \n", "NaN | \n", "alpha_chain | \n", "1 | \n", "NaN | \n", "
3 | \n", "1bd2_D-E-C-A-B_tcr_pmhc.pdb | \n", "1bd2 | \n", "tcr_pmhc | \n", "holo | \n", "D | \n", "E | \n", "C | \n", "A | \n", "B | \n", "NSMFDY-ISSIKDK-AAMEGAQKLV-MNHEY-SVGAGI-ASSYPGG... | \n", "LLFGYPVYV | \n", "hla_a_02_01 | \n", "1bd2_D-E-C-A-B_tcr_pmhc | \n", "CDR-A1 | \n", "NSMFDY | \n", "alpha_chain | \n", "1 | \n", "6.0 | \n", "
4 | \n", "1bii_P-A-B_pmhc.pdb | \n", "1bii | \n", "pmhc | \n", "apo | \n", "NaN | \n", "NaN | \n", "P | \n", "A | \n", "B | \n", "NaN | \n", "RGPGRAFVTI | \n", "h2_dd | \n", "1bii_P-A-B_pmhc | \n", "CDR-A1 | \n", "NaN | \n", "alpha_chain | \n", "1 | \n", "NaN | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
2341 | \n", "7rtd_C-A-B_pmhc.pdb | \n", "7rtd | \n", "pmhc | \n", "apo | \n", "NaN | \n", "NaN | \n", "C | \n", "A | \n", "B | \n", "NaN | \n", "YLQPRTFLL | \n", "hla_a_02_01 | \n", "7rtd_C-A-B_pmhc | \n", "CDR-B3 | \n", "NaN | \n", "beta_chain | \n", "3 | \n", "NaN | \n", "
2342 | \n", "7rtr_D-E-C-A-B_tcr_pmhc.pdb | \n", "7rtr | \n", "tcr_pmhc | \n", "holo | \n", "D | \n", "E | \n", "C | \n", "A | \n", "B | \n", "DRGSQS-IYSNGD-AVNRDDKII-SEHNR-FQNEAQ-ASSPDIEQY | \n", "YLQPRTFLL | \n", "hla_a_02_01 | \n", "7rtr_D-E-C-A-B_tcr_pmhc | \n", "CDR-B3 | \n", "ASSPDIEQY | \n", "beta_chain | \n", "3 | \n", "9.0 | \n", "
2343 | \n", "8gvb_A-B-P-H-L_tcr_pmhc.pdb | \n", "8gvb | \n", "tcr_pmhc | \n", "holo | \n", "A | \n", "B | \n", "P | \n", "H | \n", "L | \n", "YGATPY-YFSGDTLV-AVGFTGGGNKLT-SEHNR-FQNEAQ-ASSD... | \n", "RYPLTFGW | \n", "hla_a_24_02 | \n", "8gvb_A-B-P-H-L_tcr_pmhc | \n", "CDR-B3 | \n", "ASSDRDRVPETQY | \n", "beta_chain | \n", "3 | \n", "13.0 | \n", "
2344 | \n", "8gvg_A-B-P-H-L_tcr_pmhc.pdb | \n", "8gvg | \n", "tcr_pmhc | \n", "holo | \n", "A | \n", "B | \n", "P | \n", "H | \n", "L | \n", "YGATPY-YFSGDTLV-AVGFTGGGNKLT-SEHNR-FQNEAQ-ASSD... | \n", "RFPLTFGW | \n", "hla_a_24_02 | \n", "8gvg_A-B-P-H-L_tcr_pmhc | \n", "CDR-B3 | \n", "ASSDRDRVPETQY | \n", "beta_chain | \n", "3 | \n", "13.0 | \n", "
2345 | \n", "8gvi_A-B-P-H-L_tcr_pmhc.pdb | \n", "8gvi | \n", "tcr_pmhc | \n", "holo | \n", "A | \n", "B | \n", "P | \n", "H | \n", "L | \n", "YGATPY-YFSGDTLV-AVVFTGGGNKLT-SEHNR-FQNEAQ-ASSL... | \n", "RYPLTFGW | \n", "hla_a_24_02 | \n", "8gvi_A-B-P-H-L_tcr_pmhc | \n", "CDR-B3 | \n", "ASSLRDRVPETQY | \n", "beta_chain | \n", "3 | \n", "13.0 | \n", "
2346 rows × 18 columns
\n", "\n", " | complex_id | \n", "structure_x_name | \n", "structure_y_name | \n", "chain_type | \n", "cdr | \n", "residue_name | \n", "residue_seq_id | \n", "residue_insert_code | \n", "rmsd | \n", "ca_distance | \n", "chi_angle_change | \n", "com_distance | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | \n", "3qdg_D-E-C-A-B_tcr_pmhc | \n", "3qdg_D-E-C-A-B_tcr_pmhc.pdb | \n", "3qeu_A-B_tcr.pdb | \n", "alpha_chain | \n", "1 | \n", "ASP | \n", "27 | \n", "NaN | \n", "4.922807 | \n", "2.215234 | \n", "-1.001709 | \n", "3.836500 | \n", "
1 | \n", "3qdg_D-E-C-A-B_tcr_pmhc | \n", "3qdg_D-E-C-A-B_tcr_pmhc.pdb | \n", "3qeu_A-B_tcr.pdb | \n", "alpha_chain | \n", "1 | \n", "ARG | \n", "28 | \n", "NaN | \n", "7.683418 | \n", "2.322292 | \n", "-1.010462 | \n", "6.119157 | \n", "
2 | \n", "3qdg_D-E-C-A-B_tcr_pmhc | \n", "3qdg_D-E-C-A-B_tcr_pmhc.pdb | \n", "3qeu_A-B_tcr.pdb | \n", "alpha_chain | \n", "1 | \n", "GLY | \n", "29 | \n", "NaN | \n", "0.657793 | \n", "0.718576 | \n", "NaN | \n", "0.452200 | \n", "
3 | \n", "3qdg_D-E-C-A-B_tcr_pmhc | \n", "3qdg_D-E-C-A-B_tcr_pmhc.pdb | \n", "3qeu_A-B_tcr.pdb | \n", "alpha_chain | \n", "1 | \n", "SER | \n", "36 | \n", "NaN | \n", "1.224430 | \n", "0.404912 | \n", "-2.505061 | \n", "0.866544 | \n", "
4 | \n", "3qdg_D-E-C-A-B_tcr_pmhc | \n", "3qdg_D-E-C-A-B_tcr_pmhc.pdb | \n", "3qeu_A-B_tcr.pdb | \n", "alpha_chain | \n", "1 | \n", "GLN | \n", "37 | \n", "NaN | \n", "1.133408 | \n", "0.467132 | \n", "0.667185 | \n", "0.798590 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
6228 | \n", "7rtr_D-E-C-A-B_tcr_pmhc | \n", "7n1d_A-B_tcr.pdb | \n", "7rtr_D-E-C-A-B_tcr_pmhc.pdb | \n", "beta_chain | \n", "3 | \n", "ASP | \n", "109 | \n", "NaN | \n", "0.507077 | \n", "0.180564 | \n", "0.198956 | \n", "0.208659 | \n", "
6229 | \n", "7rtr_D-E-C-A-B_tcr_pmhc | \n", "7n1d_A-B_tcr.pdb | \n", "7rtr_D-E-C-A-B_tcr_pmhc.pdb | \n", "beta_chain | \n", "3 | \n", "ILE | \n", "114 | \n", "NaN | \n", "2.164965 | \n", "0.158682 | \n", "3.679442 | \n", "0.829175 | \n", "
6230 | \n", "7rtr_D-E-C-A-B_tcr_pmhc | \n", "7n1d_A-B_tcr.pdb | \n", "7rtr_D-E-C-A-B_tcr_pmhc.pdb | \n", "beta_chain | \n", "3 | \n", "GLU | \n", "115 | \n", "NaN | \n", "1.577728 | \n", "0.195887 | \n", "3.091039 | \n", "0.995351 | \n", "
6231 | \n", "7rtr_D-E-C-A-B_tcr_pmhc | \n", "7n1d_A-B_tcr.pdb | \n", "7rtr_D-E-C-A-B_tcr_pmhc.pdb | \n", "beta_chain | \n", "3 | \n", "GLN | \n", "116 | \n", "NaN | \n", "0.204783 | \n", "0.197683 | \n", "-0.014126 | \n", "0.166472 | \n", "
6232 | \n", "7rtr_D-E-C-A-B_tcr_pmhc | \n", "7n1d_A-B_tcr.pdb | \n", "7rtr_D-E-C-A-B_tcr_pmhc.pdb | \n", "beta_chain | \n", "3 | \n", "TYR | \n", "117 | \n", "NaN | \n", "0.180118 | \n", "0.164981 | \n", "-0.024244 | \n", "0.170852 | \n", "
6233 rows × 12 columns
\n", "\n", " | complex_id | \n", "structure_x_name | \n", "structure_y_name | \n", "chain_type | \n", "cdr | \n", "residue_name | \n", "residue_seq_id | \n", "residue_insert_code | \n", "rmsd | \n", "ca_distance | \n", "... | \n", "state_y | \n", "id | \n", "cdr_sequences_collated | \n", "peptide_sequence | \n", "mhc_slug | \n", "cdr_sequence | \n", "cdr_length | \n", "cdr_type | \n", "comparison | \n", "structure_comparison | \n", "
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | \n", "3qdg_D-E-C-A-B_tcr_pmhc | \n", "3qdg_D-E-C-A-B_tcr_pmhc.pdb | \n", "3qeu_A-B_tcr.pdb | \n", "alpha_chain | \n", "1 | \n", "ASP | \n", "27 | \n", "NaN | \n", "4.922807 | \n", "2.215234 | \n", "... | \n", "apo | \n", "3qdg_D-E-C-A-B_tcr_pmhc | \n", "DRGSQS-IYSNGD-AVNFGGGKLI-MRHNA-SNTAGT-ASSLSFGTEAF | \n", "ELAGIGILTV | \n", "hla_a_02_01 | \n", "DRGSQS | \n", "6.0 | \n", "CDR-A1 | \n", "apo-holo | \n", "3qdg_D-E-C-A-B_tcr_pmhc.pdb-3qeu_A-B_tcr.pdb | \n", "
36 | \n", "3qdg_D-E-C-A-B_tcr_pmhc | \n", "3qdg_D-E-C-A-B_tcr_pmhc.pdb | \n", "3qeu_A-B_tcr.pdb | \n", "alpha_chain | \n", "1 | \n", "ARG | \n", "28 | \n", "NaN | \n", "7.683418 | \n", "2.322292 | \n", "... | \n", "apo | \n", "3qdg_D-E-C-A-B_tcr_pmhc | \n", "DRGSQS-IYSNGD-AVNFGGGKLI-MRHNA-SNTAGT-ASSLSFGTEAF | \n", "ELAGIGILTV | \n", "hla_a_02_01 | \n", "DRGSQS | \n", "6.0 | \n", "CDR-A1 | \n", "apo-holo | \n", "3qdg_D-E-C-A-B_tcr_pmhc.pdb-3qeu_A-B_tcr.pdb | \n", "
72 | \n", "3qdg_D-E-C-A-B_tcr_pmhc | \n", "3qdg_D-E-C-A-B_tcr_pmhc.pdb | \n", "3qeu_A-B_tcr.pdb | \n", "alpha_chain | \n", "1 | \n", "GLY | \n", "29 | \n", "NaN | \n", "0.657793 | \n", "0.718576 | \n", "... | \n", "apo | \n", "3qdg_D-E-C-A-B_tcr_pmhc | \n", "DRGSQS-IYSNGD-AVNFGGGKLI-MRHNA-SNTAGT-ASSLSFGTEAF | \n", "ELAGIGILTV | \n", "hla_a_02_01 | \n", "DRGSQS | \n", "6.0 | \n", "CDR-A1 | \n", "apo-holo | \n", "3qdg_D-E-C-A-B_tcr_pmhc.pdb-3qeu_A-B_tcr.pdb | \n", "
108 | \n", "3qdg_D-E-C-A-B_tcr_pmhc | \n", "3qdg_D-E-C-A-B_tcr_pmhc.pdb | \n", "3qeu_A-B_tcr.pdb | \n", "alpha_chain | \n", "1 | \n", "SER | \n", "36 | \n", "NaN | \n", "1.224430 | \n", "0.404912 | \n", "... | \n", "apo | \n", "3qdg_D-E-C-A-B_tcr_pmhc | \n", "DRGSQS-IYSNGD-AVNFGGGKLI-MRHNA-SNTAGT-ASSLSFGTEAF | \n", "ELAGIGILTV | \n", "hla_a_02_01 | \n", "DRGSQS | \n", "6.0 | \n", "CDR-A1 | \n", "apo-holo | \n", "3qdg_D-E-C-A-B_tcr_pmhc.pdb-3qeu_A-B_tcr.pdb | \n", "
144 | \n", "3qdg_D-E-C-A-B_tcr_pmhc | \n", "3qdg_D-E-C-A-B_tcr_pmhc.pdb | \n", "3qeu_A-B_tcr.pdb | \n", "alpha_chain | \n", "1 | \n", "GLN | \n", "37 | \n", "NaN | \n", "1.133408 | \n", "0.467132 | \n", "... | \n", "apo | \n", "3qdg_D-E-C-A-B_tcr_pmhc | \n", "DRGSQS-IYSNGD-AVNFGGGKLI-MRHNA-SNTAGT-ASSLSFGTEAF | \n", "ELAGIGILTV | \n", "hla_a_02_01 | \n", "DRGSQS | \n", "6.0 | \n", "CDR-A1 | \n", "apo-holo | \n", "3qdg_D-E-C-A-B_tcr_pmhc.pdb-3qeu_A-B_tcr.pdb | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
158220 | \n", "7rtr_D-E-C-A-B_tcr_pmhc | \n", "7n1d_A-B_tcr.pdb | \n", "7rtr_D-E-C-A-B_tcr_pmhc.pdb | \n", "beta_chain | \n", "3 | \n", "ASP | \n", "109 | \n", "NaN | \n", "0.507077 | \n", "0.180564 | \n", "... | \n", "holo | \n", "7rtr_D-E-C-A-B_tcr_pmhc | \n", "DRGSQS-IYSNGD-AVNRDDKII-SEHNR-FQNEAQ-ASSPDIEQY | \n", "YLQPRTFLL | \n", "hla_a_02_01 | \n", "ASSPDIEQY | \n", "9.0 | \n", "CDR-B3 | \n", "apo-holo | \n", "7n1d_A-B_tcr.pdb-7rtr_D-E-C-A-B_tcr_pmhc.pdb | \n", "
158256 | \n", "7rtr_D-E-C-A-B_tcr_pmhc | \n", "7n1d_A-B_tcr.pdb | \n", "7rtr_D-E-C-A-B_tcr_pmhc.pdb | \n", "beta_chain | \n", "3 | \n", "ILE | \n", "114 | \n", "NaN | \n", "2.164965 | \n", "0.158682 | \n", "... | \n", "holo | \n", "7rtr_D-E-C-A-B_tcr_pmhc | \n", "DRGSQS-IYSNGD-AVNRDDKII-SEHNR-FQNEAQ-ASSPDIEQY | \n", "YLQPRTFLL | \n", "hla_a_02_01 | \n", "ASSPDIEQY | \n", "9.0 | \n", "CDR-B3 | \n", "apo-holo | \n", "7n1d_A-B_tcr.pdb-7rtr_D-E-C-A-B_tcr_pmhc.pdb | \n", "
158292 | \n", "7rtr_D-E-C-A-B_tcr_pmhc | \n", "7n1d_A-B_tcr.pdb | \n", "7rtr_D-E-C-A-B_tcr_pmhc.pdb | \n", "beta_chain | \n", "3 | \n", "GLU | \n", "115 | \n", "NaN | \n", "1.577728 | \n", "0.195887 | \n", "... | \n", "holo | \n", "7rtr_D-E-C-A-B_tcr_pmhc | \n", "DRGSQS-IYSNGD-AVNRDDKII-SEHNR-FQNEAQ-ASSPDIEQY | \n", "YLQPRTFLL | \n", "hla_a_02_01 | \n", "ASSPDIEQY | \n", "9.0 | \n", "CDR-B3 | \n", "apo-holo | \n", "7n1d_A-B_tcr.pdb-7rtr_D-E-C-A-B_tcr_pmhc.pdb | \n", "
158328 | \n", "7rtr_D-E-C-A-B_tcr_pmhc | \n", "7n1d_A-B_tcr.pdb | \n", "7rtr_D-E-C-A-B_tcr_pmhc.pdb | \n", "beta_chain | \n", "3 | \n", "GLN | \n", "116 | \n", "NaN | \n", "0.204783 | \n", "0.197683 | \n", "... | \n", "holo | \n", "7rtr_D-E-C-A-B_tcr_pmhc | \n", "DRGSQS-IYSNGD-AVNRDDKII-SEHNR-FQNEAQ-ASSPDIEQY | \n", "YLQPRTFLL | \n", "hla_a_02_01 | \n", "ASSPDIEQY | \n", "9.0 | \n", "CDR-B3 | \n", "apo-holo | \n", "7n1d_A-B_tcr.pdb-7rtr_D-E-C-A-B_tcr_pmhc.pdb | \n", "
158364 | \n", "7rtr_D-E-C-A-B_tcr_pmhc | \n", "7n1d_A-B_tcr.pdb | \n", "7rtr_D-E-C-A-B_tcr_pmhc.pdb | \n", "beta_chain | \n", "3 | \n", "TYR | \n", "117 | \n", "NaN | \n", "0.180118 | \n", "0.164981 | \n", "... | \n", "holo | \n", "7rtr_D-E-C-A-B_tcr_pmhc | \n", "DRGSQS-IYSNGD-AVNRDDKII-SEHNR-FQNEAQ-ASSPDIEQY | \n", "YLQPRTFLL | \n", "hla_a_02_01 | \n", "ASSPDIEQY | \n", "9.0 | \n", "CDR-B3 | \n", "apo-holo | \n", "7n1d_A-B_tcr.pdb-7rtr_D-E-C-A-B_tcr_pmhc.pdb | \n", "
4400 rows × 29 columns
\n", "\n", " | structure_x_name | \n", "structure_y_name | \n", "cdr_type | \n", "cdr | \n", "chain_type | \n", "cdr_length | \n", "apex_ca_distance | \n", "
---|---|---|---|---|---|---|---|
0 | \n", "1ao7_D-E-C-A-B_tcr_pmhc.pdb | \n", "3qh3_A-B_tcr.pdb | \n", "CDR-A1 | \n", "1 | \n", "alpha_chain | \n", "6.0 | \n", "0.153049 | \n", "
1 | \n", "1ao7_D-E-C-A-B_tcr_pmhc.pdb | \n", "3qh3_A-B_tcr.pdb | \n", "CDR-A2 | \n", "2 | \n", "alpha_chain | \n", "6.0 | \n", "0.447122 | \n", "
2 | \n", "1ao7_D-E-C-A-B_tcr_pmhc.pdb | \n", "3qh3_A-B_tcr.pdb | \n", "CDR-A3 | \n", "3 | \n", "alpha_chain | \n", "11.0 | \n", "2.461146 | \n", "
3 | \n", "1ao7_D-E-C-A-B_tcr_pmhc.pdb | \n", "3qh3_A-B_tcr.pdb | \n", "CDR-B1 | \n", "1 | \n", "beta_chain | \n", "5.0 | \n", "0.319232 | \n", "
4 | \n", "1ao7_D-E-C-A-B_tcr_pmhc.pdb | \n", "3qh3_A-B_tcr.pdb | \n", "CDR-B2 | \n", "2 | \n", "beta_chain | \n", "6.0 | \n", "0.167444 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
569 | \n", "7r7z_A-B_tcr.pdb | \n", "7r80_A-B-E-C-D_tcr_pmhc.pdb | \n", "CDR-A2 | \n", "2 | \n", "alpha_chain | \n", "7.0 | \n", "0.173771 | \n", "
570 | \n", "7r7z_A-B_tcr.pdb | \n", "7r80_A-B-E-C-D_tcr_pmhc.pdb | \n", "CDR-A3 | \n", "3 | \n", "alpha_chain | \n", "11.0 | \n", "0.508615 | \n", "
571 | \n", "7r7z_A-B_tcr.pdb | \n", "7r80_A-B-E-C-D_tcr_pmhc.pdb | \n", "CDR-B1 | \n", "1 | \n", "beta_chain | \n", "5.0 | \n", "0.108211 | \n", "
572 | \n", "7r7z_A-B_tcr.pdb | \n", "7r80_A-B-E-C-D_tcr_pmhc.pdb | \n", "CDR-B2 | \n", "2 | \n", "beta_chain | \n", "6.0 | \n", "0.219891 | \n", "
573 | \n", "7r7z_A-B_tcr.pdb | \n", "7r80_A-B-E-C-D_tcr_pmhc.pdb | \n", "CDR-B3 | \n", "3 | \n", "beta_chain | \n", "13.0 | \n", "0.789117 | \n", "
574 rows × 7 columns
\n", "\n", " | complex_id | \n", "structure_x_name | \n", "structure_y_name | \n", "rmsd | \n", "
---|---|---|---|---|
2 | \n", "5c0a_D-E-C-A-B_tcr_pmhc | \n", "5c0a_D-E-C-A-B_tcr_pmhc.pdb | \n", "5n1y_C-A-B_pmhc.pdb | \n", "0.448858 | \n", "
5 | \n", "5wlg_D-E-C-A-B_tcr_pmhc | \n", "5wlg_D-E-C-A-B_tcr_pmhc.pdb | \n", "5wli_C-A-B_pmhc.pdb | \n", "0.498148 | \n", "
8 | \n", "5wlg_D-E-C-A-B_tcr_pmhc | \n", "5wlg_D-E-C-A-B_tcr_pmhc.pdb | \n", "5wli_F-D-E_pmhc.pdb | \n", "0.519507 | \n", "
11 | \n", "5wlg_D-E-C-A-B_tcr_pmhc | \n", "5wlg_D-E-C-A-B_tcr_pmhc.pdb | \n", "5wli_I-G-H_pmhc.pdb | \n", "0.459025 | \n", "
14 | \n", "5wlg_D-E-C-A-B_tcr_pmhc | \n", "5wlg_D-E-C-A-B_tcr_pmhc.pdb | \n", "5wli_L-J-K_pmhc.pdb | \n", "0.494705 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
3301 | \n", "7rtr_D-E-C-A-B_tcr_pmhc | \n", "7n6d_O-M-N_pmhc.pdb | \n", "7rtd_C-A-B_pmhc.pdb | \n", "0.486296 | \n", "
3304 | \n", "7rtr_D-E-C-A-B_tcr_pmhc | \n", "7n6d_O-M-N_pmhc.pdb | \n", "7rtr_D-E-C-A-B_tcr_pmhc.pdb | \n", "0.448905 | \n", "
3307 | \n", "7rtr_D-E-C-A-B_tcr_pmhc | \n", "7p3d_C-A-B_pmhc.pdb | \n", "7rtd_C-A-B_pmhc.pdb | \n", "0.773692 | \n", "
3310 | \n", "7rtr_D-E-C-A-B_tcr_pmhc | \n", "7p3d_C-A-B_pmhc.pdb | \n", "7rtr_D-E-C-A-B_tcr_pmhc.pdb | \n", "0.765295 | \n", "
3313 | \n", "7rtr_D-E-C-A-B_tcr_pmhc | \n", "7rtd_C-A-B_pmhc.pdb | \n", "7rtr_D-E-C-A-B_tcr_pmhc.pdb | \n", "0.455078 | \n", "
1096 rows × 4 columns
\n", "\n", " | peptide_sequence | \n", "comparison | \n", "peptide_length | \n", "mhc_slug | \n", "rmsd | \n", "
---|---|---|---|---|---|
0 | \n", "AAGIGILTV | \n", "apo-holo | \n", "9.0 | \n", "hla_a_02_01 | \n", "1.025622 | \n", "
1 | \n", "ALGIGILTV | \n", "apo-holo | \n", "9.0 | \n", "hla_a_02_01 | \n", "1.274516 | \n", "
2 | \n", "ALWGFFPVL | \n", "apo-holo | \n", "9.0 | \n", "hla_a_02_01 | \n", "0.351748 | \n", "
3 | \n", "ALWGPDPAAA | \n", "apo-holo | \n", "10.0 | \n", "hla_a_02_01 | \n", "0.703094 | \n", "
4 | \n", "APRGPHGGAASGL | \n", "apo-holo | \n", "13.0 | \n", "hla_b_07_02 | \n", "3.523593 | \n", "
... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
75 | \n", "VVVGAGGVGK | \n", "apo-holo | \n", "10.0 | \n", "hla_a_11_01 | \n", "1.483028 | \n", "
76 | \n", "YGFRNVVHI | \n", "apo-holo | \n", "9.0 | \n", "h2_db | \n", "0.275006 | \n", "
77 | \n", "YLGGPDFPTI | \n", "apo-holo | \n", "10.0 | \n", "hla_a_02_01 | \n", "0.868938 | \n", "
78 | \n", "YLQPRTFLL | \n", "apo-holo | \n", "9.0 | \n", "hla_a_02_01 | \n", "0.584577 | \n", "
79 | \n", "YQFGPDFPIA | \n", "apo-holo | \n", "10.0 | \n", "hla_a_02_01 | \n", "0.408370 | \n", "
80 rows × 5 columns
\n", "