# By using this file you agree to the legally binding terms of use found at # https://github.com/google-deepmind/alphafold3/blob/main/OUTPUT_TERMS_OF_USE.md. # To request access to the AlphaFold 3 model parameters, follow the process set # out at https://github.com/google-deepmind/alphafold3. You may only use these if # received directly from Google. Use is subject to terms of use available at # https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md. data_spkb23305 # _entry.id spkb23305 # loop_ _atom_type.symbol C N O S # loop_ _audit_author.name _audit_author.pdbx_ordinal "Google DeepMind" 1 "Isomorphic Labs" 2 # _audit_conform.dict_location https://raw.githubusercontent.com/ihmwg/ModelCIF/master/dist/mmcif_ma.dic _audit_conform.dict_name mmcif_ma.dic _audit_conform.dict_version 1.4.5 # loop_ _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_smiles _chem_comp.pdbx_synonyms _chem_comp.type "C3 H7 N O2" 89.093 ALA y ALANINE C[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" "C6 H13 N O2" 131.173 LEU y LEUCINE CC(C)C[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" "C6 H15 N2 O2" 147.195 LYS y LYSINE C(CC[NH3+])C[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" "C5 H11 N O2 S" 149.211 MET y METHIONINE CSCC[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" "C9 H11 N O2" 165.189 PHE y PHENYLALANINE c1ccc(cc1)C[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" "C5 H9 N O2" 115.130 PRO y PROLINE C1C[C@H](NC1)C(=O)O ? "L-PEPTIDE LINKING" "C9 H11 N O3" 181.189 TYR y TYROSINE c1cc(ccc1C[C@@H](C(=O)O)N)O ? "L-PEPTIDE LINKING" # _citation.book_publisher ? _citation.country UK _citation.id primary _citation.journal_full Nature _citation.journal_id_ASTM NATUAS _citation.journal_id_CSD 0006 _citation.journal_id_ISSN 0028-0836 _citation.journal_volume 630 _citation.page_first 493 _citation.page_last 500 _citation.pdbx_database_id_DOI 10.1038/s41586-024-07487-w _citation.pdbx_database_id_PubMed 38718835 _citation.title "Accurate structure prediction of biomolecular interactions with AlphaFold 3" _citation.year 2024 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary "Google DeepMind" 1 primary "Isomorphic Labs" 2 # _entity.id 1 _entity.pdbx_description . _entity.type polymer # _entity_poly.entity_id 1 _entity_poly.pdbx_strand_id A _entity_poly.type polypeptide(L) # loop_ _entity_poly_seq.entity_id _entity_poly_seq.hetero _entity_poly_seq.mon_id _entity_poly_seq.num 1 n MET 1 1 n LYS 2 1 n LYS 3 1 n TYR 4 1 n LEU 5 1 n LEU 6 1 n LEU 7 1 n ALA 8 1 n LEU 9 1 n LEU 10 1 n PRO 11 1 n PHE 12 1 n LEU 13 1 n TYR 14 1 n ALA 15 # _ma_data.content_type "model coordinates" _ma_data.id 1 _ma_data.name Model # _ma_model_list.data_id 1 _ma_model_list.model_group_id 1 _ma_model_list.model_group_name "AlphaFold-beta-20231127 (3.0.0 @ 2025-07-05 08:38:17)" _ma_model_list.model_id 1 _ma_model_list.model_name "Top ranked model" _ma_model_list.model_type "Ab initio model" _ma_model_list.ordinal_id 1 # loop_ _ma_protocol_step.method_type _ma_protocol_step.ordinal_id _ma_protocol_step.protocol_id _ma_protocol_step.step_id "coevolution MSA" 1 1 1 "template search" 2 1 2 modeling 3 1 3 # loop_ _ma_qa_metric.id _ma_qa_metric.mode _ma_qa_metric.name _ma_qa_metric.software_group_id _ma_qa_metric.type 1 global pLDDT 1 pLDDT 2 local pLDDT 1 pLDDT # _ma_qa_metric_global.metric_id 1 _ma_qa_metric_global.metric_value 88.21 _ma_qa_metric_global.model_id 1 _ma_qa_metric_global.ordinal_id 1 # loop_ _ma_qa_metric_local.label_asym_id _ma_qa_metric_local.label_comp_id _ma_qa_metric_local.label_seq_id _ma_qa_metric_local.metric_id _ma_qa_metric_local.metric_value _ma_qa_metric_local.model_id _ma_qa_metric_local.ordinal_id A MET 1 2 84.32 1 1 A LYS 2 2 82.47 1 2 A LYS 3 2 82.41 1 3 A TYR 4 2 89.33 1 4 A LEU 5 2 90.72 1 5 A LEU 6 2 91.51 1 6 A LEU 7 2 91.71 1 7 A ALA 8 2 94.65 1 8 A LEU 9 2 91.85 1 9 A LEU 10 2 89.66 1 10 A PRO 11 2 92.25 1 11 A PHE 12 2 87.21 1 12 A LEU 13 2 86.44 1 13 A TYR 14 2 86.76 1 14 A ALA 15 2 86.23 1 15 # _ma_software_group.group_id 1 _ma_software_group.ordinal_id 1 _ma_software_group.software_id 1 # _ma_target_entity.data_id 1 _ma_target_entity.entity_id 1 _ma_target_entity.origin . # _ma_target_entity_instance.asym_id A _ma_target_entity_instance.details . _ma_target_entity_instance.entity_id 1 # loop_ _pdbx_data_usage.details _pdbx_data_usage.id _pdbx_data_usage.type _pdbx_data_usage.url ;Non-commercial use only, by using this file you agree to the terms of use found at https://github.com/google-deepmind/alphafold3/blob/main/OUTPUT_TERMS_OF_USE.md. To request access to the AlphaFold 3 model parameters, follow the process set out at https://github.com/google-deepmind/alphafold3. You may only use these if received directly from Google. Use is subject to terms of use available at https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md. ; 1 license https://github.com/google-deepmind/alphafold3/blob/main/OUTPUT_TERMS_OF_USE.md ;AlphaFold 3 and its output are not intended for, have not been validated for, and are not approved for clinical use. They are provided "as-is" without any warranty of any kind, whether expressed or implied. No warranty is given that use shall not infringe the rights of any third party. ; 2 disclaimer ? # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.hetero _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.seq_id A 1 1 n MET . 1 A 1 A 2 1 n LYS . 2 A 2 A 3 1 n LYS . 3 A 3 A 4 1 n TYR . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n PRO . 11 A 11 A 12 1 n PHE . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n TYR . 14 A 14 A 15 1 n ALA . 15 A 15 # _software.classification other _software.date ? _software.description "Structure prediction" _software.name AlphaFold _software.pdbx_ordinal 1 _software.type package _software.version "AlphaFold-beta-20231127 (9ceee3b5f7825b611ab42eaad843248507ced2da1e745fa3b3d93c6c4ad3ca74)" # _struct_asym.entity_id 1 _struct_asym.id A # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num ATOM 1 N N . MET A 1 1 ? 0.205 0.457 11.640 1.00 88.91 1 A 1 ATOM 2 C CA . MET A 1 1 ? 1.303 1.205 11.006 1.00 90.94 1 A 1 ATOM 3 C C . MET A 1 1 ? 0.952 1.594 9.573 1.00 91.24 1 A 1 ATOM 4 O O . MET A 1 1 ? 0.116 0.959 8.940 1.00 89.61 1 A 1 ATOM 5 C CB . MET A 1 1 ? 2.583 0.363 11.005 1.00 86.29 1 A 1 ATOM 6 C CG . MET A 1 1 ? 3.325 0.432 12.339 1.00 79.58 1 A 1 ATOM 7 S SD . MET A 1 1 ? 2.709 -0.770 13.512 1.00 77.72 1 A 1 ATOM 8 C CE . MET A 1 1 ? 3.669 -0.331 14.958 1.00 70.28 1 A 1 ATOM 9 N N . LYS A 1 2 ? 1.595 2.631 9.055 1.00 89.60 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 1.357 3.118 7.698 1.00 90.33 2 A 1 ATOM 11 C C . LYS A 1 2 ? 2.131 2.312 6.656 1.00 90.89 2 A 1 ATOM 12 O O . LYS A 1 2 ? 1.951 2.514 5.457 1.00 89.44 2 A 1 ATOM 13 C CB . LYS A 1 2 ? 1.757 4.590 7.615 1.00 88.30 2 A 1 ATOM 14 C CG . LYS A 1 2 ? 0.813 5.510 8.374 1.00 80.35 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 1.393 6.903 8.496 1.00 78.63 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 0.492 7.797 9.325 1.00 71.15 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 1.166 9.095 9.617 1.00 63.55 2 A 1 ATOM 18 N N . LYS A 1 3 ? 2.978 1.417 7.113 1.00 89.49 3 A 1 ATOM 19 C CA . LYS A 1 3 ? 3.785 0.594 6.210 1.00 90.45 3 A 1 ATOM 20 C C . LYS A 1 3 ? 2.898 -0.326 5.369 1.00 92.00 3 A 1 ATOM 21 O O . LYS A 1 3 ? 3.144 -0.525 4.185 1.00 90.63 3 A 1 ATOM 22 C CB . LYS A 1 3 ? 4.792 -0.237 7.017 1.00 88.61 3 A 1 ATOM 23 C CG . LYS A 1 3 ? 6.046 0.544 7.396 1.00 80.95 3 A 1 ATOM 24 C CD . LYS A 1 3 ? 7.025 -0.321 8.179 1.00 77.68 3 A 1 ATOM 25 C CE . LYS A 1 3 ? 8.349 0.401 8.397 1.00 69.85 3 A 1 ATOM 26 N NZ . LYS A 1 3 ? 9.302 -0.442 9.182 1.00 62.00 3 A 1 ATOM 27 N N . TYR A 1 4 ? 1.875 -0.886 5.986 1.00 90.82 4 A 1 ATOM 28 C CA . TYR A 1 4 ? 0.962 -1.786 5.288 1.00 91.77 4 A 1 ATOM 29 C C . TYR A 1 4 ? -0.007 -1.010 4.401 1.00 92.94 4 A 1 ATOM 30 O O . TYR A 1 4 ? -0.514 -1.537 3.410 1.00 91.57 4 A 1 ATOM 31 C CB . TYR A 1 4 ? 0.184 -2.621 6.312 1.00 90.94 4 A 1 ATOM 32 C CG . TYR A 1 4 ? 1.051 -3.660 6.996 1.00 90.66 4 A 1 ATOM 33 C CD1 . TYR A 1 4 ? 1.816 -3.342 8.108 1.00 87.76 4 A 1 ATOM 34 C CD2 . TYR A 1 4 ? 1.094 -4.964 6.517 1.00 88.07 4 A 1 ATOM 35 C CE1 . TYR A 1 4 ? 2.614 -4.293 8.733 1.00 86.54 4 A 1 ATOM 36 C CE2 . TYR A 1 4 ? 1.885 -5.928 7.137 1.00 87.17 4 A 1 ATOM 37 C CZ . TYR A 1 4 ? 2.640 -5.584 8.246 1.00 87.68 4 A 1 ATOM 38 O OH . TYR A 1 4 ? 3.424 -6.537 8.863 1.00 86.00 4 A 1 ATOM 39 N N . LEU A 1 5 ? -0.255 0.240 4.748 1.00 93.63 5 A 1 ATOM 40 C CA . LEU A 1 5 ? -1.160 1.093 3.983 1.00 93.57 5 A 1 ATOM 41 C C . LEU A 1 5 ? -0.515 1.533 2.677 1.00 94.47 5 A 1 ATOM 42 O O . LEU A 1 5 ? -1.179 1.620 1.641 1.00 93.81 5 A 1 ATOM 43 C CB . LEU A 1 5 ? -1.547 2.311 4.823 1.00 93.16 5 A 1 ATOM 44 C CG . LEU A 1 5 ? -3.027 2.656 4.807 1.00 88.53 5 A 1 ATOM 45 C CD1 . LEU A 1 5 ? -3.384 3.526 6.000 1.00 84.19 5 A 1 ATOM 46 C CD2 . LEU A 1 5 ? -3.399 3.376 3.521 1.00 84.38 5 A 1 ATOM 47 N N . LEU A 1 6 ? 0.775 1.803 2.723 1.00 94.04 6 A 1 ATOM 48 C CA . LEU A 1 6 ? 1.517 2.233 1.542 1.00 94.22 6 A 1 ATOM 49 C C . LEU A 1 6 ? 1.568 1.130 0.494 1.00 94.90 6 A 1 ATOM 50 O O . LEU A 1 6 ? 1.583 1.408 -0.706 1.00 94.44 6 A 1 ATOM 51 C CB . LEU A 1 6 ? 2.937 2.634 1.952 1.00 94.09 6 A 1 ATOM 52 C CG . LEU A 1 6 ? 3.038 4.014 2.591 1.00 89.23 6 A 1 ATOM 53 C CD1 . LEU A 1 6 ? 4.226 4.082 3.531 1.00 85.56 6 A 1 ATOM 54 C CD2 . LEU A 1 6 ? 3.167 5.082 1.515 1.00 85.59 6 A 1 ATOM 55 N N . LEU A 1 7 ? 1.598 -0.107 0.947 1.00 94.96 7 A 1 ATOM 56 C CA . LEU A 1 7 ? 1.650 -1.255 0.047 1.00 94.54 7 A 1 ATOM 57 C C . LEU A 1 7 ? 0.333 -1.429 -0.698 1.00 95.04 7 A 1 ATOM 58 O O . LEU A 1 7 ? 0.311 -1.953 -1.809 1.00 94.67 7 A 1 ATOM 59 C CB . LEU A 1 7 ? 1.971 -2.517 0.849 1.00 94.07 7 A 1 ATOM 60 C CG . LEU A 1 7 ? 2.486 -3.675 0.006 1.00 88.44 7 A 1 ATOM 61 C CD1 . LEU A 1 7 ? 3.965 -3.477 -0.309 1.00 85.94 7 A 1 ATOM 62 C CD2 . LEU A 1 7 ? 2.280 -4.993 0.722 1.00 85.98 7 A 1 ATOM 63 N N . ALA A 1 8 ? -0.750 -0.982 -0.104 1.00 95.17 8 A 1 ATOM 64 C CA . ALA A 1 8 ? -2.075 -1.101 -0.700 1.00 94.93 8 A 1 ATOM 65 C C . ALA A 1 8 ? -2.446 0.133 -1.520 1.00 95.35 8 A 1 ATOM 66 O O . ALA A 1 8 ? -3.509 0.174 -2.138 1.00 93.66 8 A 1 ATOM 67 C CB . ALA A 1 8 ? -3.101 -1.334 0.405 1.00 94.12 8 A 1 ATOM 68 N N . LEU A 1 9 ? -1.564 1.116 -1.533 1.00 94.77 9 A 1 ATOM 69 C CA . LEU A 1 9 ? -1.811 2.355 -2.266 1.00 94.30 9 A 1 ATOM 70 C C . LEU A 1 9 ? -1.379 2.233 -3.721 1.00 94.90 9 A 1 ATOM 71 O O . LEU A 1 9 ? -2.034 2.774 -4.616 1.00 93.47 9 A 1 ATOM 72 C CB . LEU A 1 9 ? -1.067 3.513 -1.589 1.00 93.83 9 A 1 ATOM 73 C CG . LEU A 1 9 ? -1.911 4.306 -0.596 1.00 90.74 9 A 1 ATOM 74 C CD1 . LEU A 1 9 ? -1.029 5.037 0.404 1.00 86.12 9 A 1 ATOM 75 C CD2 . LEU A 1 9 ? -2.799 5.295 -1.332 1.00 86.67 9 A 1 ATOM 76 N N . LEU A 1 10 ? -0.294 1.527 -3.956 1.00 93.02 10 A 1 ATOM 77 C CA . LEU A 1 10 ? 0.223 1.332 -5.305 1.00 92.63 10 A 1 ATOM 78 C C . LEU A 1 10 ? -0.755 0.562 -6.193 1.00 93.52 10 A 1 ATOM 79 O O . LEU A 1 10 ? -1.079 1.012 -7.293 1.00 91.91 10 A 1 ATOM 80 C CB . LEU A 1 10 ? 1.570 0.606 -5.248 1.00 91.60 10 A 1 ATOM 81 C CG . LEU A 1 10 ? 2.676 1.316 -6.018 1.00 88.01 10 A 1 ATOM 82 C CD1 . LEU A 1 10 ? 3.295 2.414 -5.164 1.00 83.05 10 A 1 ATOM 83 C CD2 . LEU A 1 10 ? 3.736 0.318 -6.445 1.00 83.54 10 A 1 ATOM 84 N N . PRO A 1 11 ? -1.219 -0.606 -5.746 1.00 93.89 11 A 1 ATOM 85 C CA . PRO A 1 11 ? -2.162 -1.410 -6.536 1.00 92.75 11 A 1 ATOM 86 C C . PRO A 1 11 ? -3.503 -0.715 -6.735 1.00 93.35 11 A 1 ATOM 87 O O . PRO A 1 11 ? -4.231 -1.034 -7.672 1.00 91.47 11 A 1 ATOM 88 C CB . PRO A 1 11 ? -2.325 -2.684 -5.703 1.00 90.83 11 A 1 ATOM 89 C CG . PRO A 1 11 ? -1.906 -2.316 -4.335 1.00 90.02 11 A 1 ATOM 90 C CD . PRO A 1 11 ? -0.850 -1.266 -4.495 1.00 93.44 11 A 1 ATOM 91 N N . PHE A 1 12 ? -3.833 0.212 -5.882 1.00 91.01 12 A 1 ATOM 92 C CA . PHE A 1 12 ? -5.085 0.954 -5.981 1.00 91.02 12 A 1 ATOM 93 C C . PHE A 1 12 ? -5.105 1.808 -7.241 1.00 92.39 12 A 1 ATOM 94 O O . PHE A 1 12 ? -6.137 1.919 -7.905 1.00 89.42 12 A 1 ATOM 95 C CB . PHE A 1 12 ? -5.262 1.841 -4.752 1.00 89.46 12 A 1 ATOM 96 C CG . PHE A 1 12 ? -6.433 1.442 -3.898 1.00 87.12 12 A 1 ATOM 97 C CD1 . PHE A 1 12 ? -6.394 0.288 -3.138 1.00 84.20 12 A 1 ATOM 98 C CD2 . PHE A 1 12 ? -7.574 2.232 -3.862 1.00 84.59 12 A 1 ATOM 99 C CE1 . PHE A 1 12 ? -7.476 -0.083 -2.352 1.00 83.24 12 A 1 ATOM 100 C CE2 . PHE A 1 12 ? -8.661 1.870 -3.076 1.00 83.46 12 A 1 ATOM 101 C CZ . PHE A 1 12 ? -8.610 0.708 -2.317 1.00 83.43 12 A 1 ATOM 102 N N . LEU A 1 13 ? -3.965 2.397 -7.564 1.00 89.84 13 A 1 ATOM 103 C CA . LEU A 1 13 ? -3.836 3.232 -8.751 1.00 89.47 13 A 1 ATOM 104 C C . LEU A 1 13 ? -3.678 2.388 -10.009 1.00 90.69 13 A 1 ATOM 105 O O . LEU A 1 13 ? -3.941 2.854 -11.119 1.00 88.52 13 A 1 ATOM 106 C CB . LEU A 1 13 ? -2.632 4.174 -8.596 1.00 88.21 13 A 1 ATOM 107 C CG . LEU A 1 13 ? -2.961 5.585 -8.103 1.00 85.32 13 A 1 ATOM 108 C CD1 . LEU A 1 13 ? -3.842 6.305 -9.102 1.00 80.33 13 A 1 ATOM 109 C CD2 . LEU A 1 13 ? -3.626 5.536 -6.745 1.00 79.10 13 A 1 ATOM 110 N N . TYR A 1 14 ? -3.226 1.158 -9.833 1.00 92.44 14 A 1 ATOM 111 C CA . TYR A 1 14 ? -3.012 0.241 -10.948 1.00 90.80 14 A 1 ATOM 112 C C . TYR A 1 14 ? -4.237 -0.632 -11.207 1.00 91.34 14 A 1 ATOM 113 O O . TYR A 1 14 ? -4.266 -1.389 -12.176 1.00 89.56 14 A 1 ATOM 114 C CB . TYR A 1 14 ? -1.797 -0.650 -10.644 1.00 89.32 14 A 1 ATOM 115 C CG . TYR A 1 14 ? -0.695 -0.496 -11.665 1.00 86.14 14 A 1 ATOM 116 C CD1 . TYR A 1 14 ? -0.630 -1.336 -12.762 1.00 84.78 14 A 1 ATOM 117 C CD2 . TYR A 1 14 ? 0.273 0.485 -11.517 1.00 84.33 14 A 1 ATOM 118 C CE1 . TYR A 1 14 ? 0.386 -1.201 -13.700 1.00 83.90 14 A 1 ATOM 119 C CE2 . TYR A 1 14 ? 1.292 0.633 -12.452 1.00 83.45 14 A 1 ATOM 120 C CZ . TYR A 1 14 ? 1.340 -0.214 -13.540 1.00 83.19 14 A 1 ATOM 121 O OH . TYR A 1 14 ? 2.346 -0.075 -14.464 1.00 81.88 14 A 1 ATOM 122 N N . ALA A 1 15 ? -5.226 -0.527 -10.354 1.00 91.65 15 A 1 ATOM 123 C CA . ALA A 1 15 ? -6.438 -1.339 -10.470 1.00 89.86 15 A 1 ATOM 124 C C . ALA A 1 15 ? -7.489 -0.622 -11.312 1.00 87.77 15 A 1 ATOM 125 O O . ALA A 1 15 ? -7.820 -1.111 -12.411 1.00 83.80 15 A 1 ATOM 126 C CB . ALA A 1 15 ? -6.984 -1.665 -9.085 1.00 86.01 15 A 1 ATOM 127 O OXT . ALA A 1 15 ? -7.995 0.399 -10.868 1.00 78.31 15 A 1 #