# 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_spkb13162 # _entry.id spkb13162 # 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" "C3 H7 N O2 S" 121.158 CYS y CYSTEINE C([C@@H](C(=O)O)N)S ? "L-PEPTIDE LINKING" "C6 H13 N O2" 131.173 LEU y LEUCINE CC(C)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" "C3 H7 N O3" 105.093 SER y SERINE C([C@@H](C(=O)O)N)O ? "L-PEPTIDE LINKING" "C11 H12 N2 O2" 204.225 TRP y TRYPTOPHAN c1ccc2c(c1)c(c[nH]2)C[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" "C5 H11 N O2" 117.146 VAL y VALINE CC(C)[C@@H](C(=O)O)N ? "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 TRP 2 1 n CYS 3 1 n PHE 4 1 n VAL 5 1 n PHE 6 1 n PHE 7 1 n SER 8 1 n LEU 9 1 n LEU 10 1 n ALA 11 1 n SER 12 1 n PHE 13 1 n SER 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 @ 2025-07-08 07:08:35)" _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 89.05 _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 81.41 1 1 A TRP 2 2 87.45 1 2 A CYS 3 2 91.61 1 3 A PHE 4 2 90.09 1 4 A VAL 5 2 94.45 1 5 A PHE 6 2 90.82 1 6 A PHE 7 2 90.30 1 7 A SER 8 2 91.59 1 8 A LEU 9 2 91.71 1 9 A LEU 10 2 91.06 1 10 A ALA 11 2 93.84 1 11 A SER 12 2 92.01 1 12 A PHE 13 2 85.26 1 13 A SER 14 2 86.61 1 14 A ALA 15 2 80.30 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 TRP . 2 A 2 A 3 1 n CYS . 3 A 3 A 4 1 n PHE . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n PHE . 6 A 6 A 7 1 n PHE . 7 A 7 A 8 1 n SER . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n SER . 12 A 12 A 13 1 n PHE . 13 A 13 A 14 1 n SER . 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 ? -1.668 6.756 12.212 1.00 87.92 1 A 1 ATOM 2 C CA . MET A 1 1 ? -1.441 5.368 11.777 1.00 88.11 1 A 1 ATOM 3 C C . MET A 1 1 ? -0.948 5.315 10.325 1.00 89.10 1 A 1 ATOM 4 O O . MET A 1 1 ? -1.734 5.458 9.391 1.00 86.74 1 A 1 ATOM 5 C CB . MET A 1 1 ? -2.724 4.561 11.910 1.00 83.05 1 A 1 ATOM 6 C CG . MET A 1 1 ? -2.939 4.016 13.320 1.00 77.11 1 A 1 ATOM 7 S SD . MET A 1 1 ? -3.630 5.230 14.428 1.00 73.63 1 A 1 ATOM 8 C CE . MET A 1 1 ? -3.929 4.217 15.871 1.00 65.59 1 A 1 ATOM 9 N N . TRP A 1 2 ? 0.357 5.118 10.143 1.00 91.61 2 A 1 ATOM 10 C CA . TRP A 1 2 ? 0.974 5.080 8.823 1.00 93.04 2 A 1 ATOM 11 C C . TRP A 1 2 ? 1.106 3.650 8.286 1.00 94.11 2 A 1 ATOM 12 O O . TRP A 1 2 ? 1.078 3.422 7.085 1.00 92.86 2 A 1 ATOM 13 C CB . TRP A 1 2 ? 2.353 5.747 8.883 1.00 91.41 2 A 1 ATOM 14 C CG . TRP A 1 2 ? 2.496 6.900 7.929 1.00 87.77 2 A 1 ATOM 15 C CD1 . TRP A 1 2 ? 2.555 8.215 8.246 1.00 85.40 2 A 1 ATOM 16 C CD2 . TRP A 1 2 ? 2.614 6.839 6.493 1.00 87.27 2 A 1 ATOM 17 N NE1 . TRP A 1 2 ? 2.700 8.977 7.108 1.00 83.38 2 A 1 ATOM 18 C CE2 . TRP A 1 2 ? 2.736 8.161 6.012 1.00 87.18 2 A 1 ATOM 19 C CE3 . TRP A 1 2 ? 2.628 5.795 5.571 1.00 84.95 2 A 1 ATOM 20 C CZ2 . TRP A 1 2 ? 2.873 8.448 4.653 1.00 84.43 2 A 1 ATOM 21 C CZ3 . TRP A 1 2 ? 2.762 6.085 4.215 1.00 80.70 2 A 1 ATOM 22 C CH2 . TRP A 1 2 ? 2.885 7.394 3.769 1.00 80.12 2 A 1 ATOM 23 N N . CYS A 1 3 ? 1.230 2.699 9.182 1.00 93.71 3 A 1 ATOM 24 C CA . CYS A 1 3 ? 1.374 1.289 8.816 1.00 93.75 3 A 1 ATOM 25 C C . CYS A 1 3 ? 0.155 0.763 8.054 1.00 94.70 3 A 1 ATOM 26 O O . CYS A 1 3 ? 0.281 -0.118 7.209 1.00 92.41 3 A 1 ATOM 27 C CB . CYS A 1 3 ? 1.618 0.444 10.071 1.00 90.55 3 A 1 ATOM 28 S SG . CYS A 1 3 ? 3.349 0.430 10.595 1.00 84.53 3 A 1 ATOM 29 N N . PHE A 1 4 ? -1.019 1.313 8.355 1.00 92.33 4 A 1 ATOM 30 C CA . PHE A 1 4 ? -2.251 0.899 7.695 1.00 94.03 4 A 1 ATOM 31 C C . PHE A 1 4 ? -2.280 1.361 6.241 1.00 95.48 4 A 1 ATOM 32 O O . PHE A 1 4 ? -2.717 0.624 5.352 1.00 94.81 4 A 1 ATOM 33 C CB . PHE A 1 4 ? -3.462 1.459 8.446 1.00 93.05 4 A 1 ATOM 34 C CG . PHE A 1 4 ? -4.125 0.450 9.354 1.00 89.94 4 A 1 ATOM 35 C CD1 . PHE A 1 4 ? -4.697 -0.697 8.827 1.00 87.26 4 A 1 ATOM 36 C CD2 . PHE A 1 4 ? -4.187 0.663 10.725 1.00 86.78 4 A 1 ATOM 37 C CE1 . PHE A 1 4 ? -5.312 -1.627 9.651 1.00 85.74 4 A 1 ATOM 38 C CE2 . PHE A 1 4 ? -4.804 -0.263 11.553 1.00 85.80 4 A 1 ATOM 39 C CZ . PHE A 1 4 ? -5.366 -1.411 11.018 1.00 85.75 4 A 1 ATOM 40 N N . VAL A 1 5 ? -1.806 2.559 5.990 1.00 95.16 5 A 1 ATOM 41 C CA . VAL A 1 5 ? -1.783 3.137 4.648 1.00 95.63 5 A 1 ATOM 42 C C . VAL A 1 5 ? -0.716 2.466 3.783 1.00 96.10 5 A 1 ATOM 43 O O . VAL A 1 5 ? -0.907 2.276 2.580 1.00 95.56 5 A 1 ATOM 44 C CB . VAL A 1 5 ? -1.543 4.657 4.711 1.00 95.14 5 A 1 ATOM 45 C CG1 . VAL A 1 5 ? -1.668 5.285 3.334 1.00 91.85 5 A 1 ATOM 46 C CG2 . VAL A 1 5 ? -2.518 5.317 5.675 1.00 91.69 5 A 1 ATOM 47 N N . PHE A 1 6 ? 0.388 2.111 4.404 1.00 93.76 6 A 1 ATOM 48 C CA . PHE A 1 6 ? 1.501 1.467 3.711 1.00 94.13 6 A 1 ATOM 49 C C . PHE A 1 6 ? 1.097 0.100 3.161 1.00 95.02 6 A 1 ATOM 50 O O . PHE A 1 6 ? 1.427 -0.250 2.031 1.00 94.65 6 A 1 ATOM 51 C CB . PHE A 1 6 ? 2.685 1.331 4.670 1.00 93.69 6 A 1 ATOM 52 C CG . PHE A 1 6 ? 4.017 1.314 3.966 1.00 91.08 6 A 1 ATOM 53 C CD1 . PHE A 1 6 ? 4.531 2.474 3.403 1.00 88.39 6 A 1 ATOM 54 C CD2 . PHE A 1 6 ? 4.744 0.139 3.881 1.00 88.44 6 A 1 ATOM 55 C CE1 . PHE A 1 6 ? 5.754 2.465 2.754 1.00 86.60 6 A 1 ATOM 56 C CE2 . PHE A 1 6 ? 5.971 0.125 3.229 1.00 86.62 6 A 1 ATOM 57 C CZ . PHE A 1 6 ? 6.476 1.285 2.667 1.00 86.61 6 A 1 ATOM 58 N N . PHE A 1 7 ? 0.375 -0.666 3.955 1.00 94.14 7 A 1 ATOM 59 C CA . PHE A 1 7 ? -0.076 -2.000 3.559 1.00 93.85 7 A 1 ATOM 60 C C . PHE A 1 7 ? -1.167 -1.912 2.493 1.00 94.89 7 A 1 ATOM 61 O O . PHE A 1 7 ? -1.243 -2.751 1.595 1.00 94.24 7 A 1 ATOM 62 C CB . PHE A 1 7 ? -0.597 -2.756 4.785 1.00 93.19 7 A 1 ATOM 63 C CG . PHE A 1 7 ? -0.115 -4.185 4.859 1.00 90.37 7 A 1 ATOM 64 C CD1 . PHE A 1 7 ? -0.396 -5.080 3.843 1.00 87.73 7 A 1 ATOM 65 C CD2 . PHE A 1 7 ? 0.615 -4.624 5.956 1.00 87.68 7 A 1 ATOM 66 C CE1 . PHE A 1 7 ? 0.047 -6.389 3.904 1.00 86.13 7 A 1 ATOM 67 C CE2 . PHE A 1 7 ? 1.057 -5.938 6.026 1.00 85.97 7 A 1 ATOM 68 C CZ . PHE A 1 7 ? 0.774 -6.820 5.000 1.00 85.15 7 A 1 ATOM 69 N N . SER A 1 8 ? -2.005 -0.889 2.583 1.00 93.02 8 A 1 ATOM 70 C CA . SER A 1 8 ? -3.101 -0.681 1.642 1.00 92.99 8 A 1 ATOM 71 C C . SER A 1 8 ? -2.573 -0.320 0.254 1.00 93.42 8 A 1 ATOM 72 O O . SER A 1 8 ? -3.094 -0.789 -0.760 1.00 92.31 8 A 1 ATOM 73 C CB . SER A 1 8 ? -4.036 0.413 2.157 1.00 92.86 8 A 1 ATOM 74 O OG . SER A 1 8 ? -5.384 0.010 2.104 1.00 84.93 8 A 1 ATOM 75 N N . LEU A 1 9 ? -1.525 0.494 0.215 1.00 94.90 9 A 1 ATOM 76 C CA . LEU A 1 9 ? -0.918 0.914 -1.044 1.00 94.58 9 A 1 ATOM 77 C C . LEU A 1 9 ? -0.205 -0.243 -1.733 1.00 95.37 9 A 1 ATOM 78 O O . LEU A 1 9 ? -0.242 -0.364 -2.960 1.00 94.81 9 A 1 ATOM 79 C CB . LEU A 1 9 ? 0.067 2.059 -0.779 1.00 94.34 9 A 1 ATOM 80 C CG . LEU A 1 9 ? -0.553 3.454 -0.783 1.00 88.14 9 A 1 ATOM 81 C CD1 . LEU A 1 9 ? 0.308 4.434 -0.012 1.00 85.57 9 A 1 ATOM 82 C CD2 . LEU A 1 9 ? -0.748 3.942 -2.210 1.00 85.99 9 A 1 ATOM 83 N N . LEU A 1 10 ? 0.436 -1.078 -0.947 1.00 94.95 10 A 1 ATOM 84 C CA . LEU A 1 10 ? 1.163 -2.232 -1.468 1.00 94.10 10 A 1 ATOM 85 C C . LEU A 1 10 ? 0.213 -3.253 -2.088 1.00 94.42 10 A 1 ATOM 86 O O . LEU A 1 10 ? 0.504 -3.824 -3.138 1.00 94.01 10 A 1 ATOM 87 C CB . LEU A 1 10 ? 1.981 -2.884 -0.348 1.00 93.59 10 A 1 ATOM 88 C CG . LEU A 1 10 ? 3.331 -3.449 -0.790 1.00 88.07 10 A 1 ATOM 89 C CD1 . LEU A 1 10 ? 4.397 -2.358 -0.821 1.00 84.69 10 A 1 ATOM 90 C CD2 . LEU A 1 10 ? 3.761 -4.572 0.128 1.00 84.66 10 A 1 ATOM 91 N N . ALA A 1 11 ? -0.915 -3.491 -1.444 1.00 94.59 11 A 1 ATOM 92 C CA . ALA A 1 11 ? -1.909 -4.453 -1.917 1.00 94.14 11 A 1 ATOM 93 C C . ALA A 1 11 ? -2.626 -3.950 -3.170 1.00 94.79 11 A 1 ATOM 94 O O . ALA A 1 11 ? -2.957 -4.732 -4.059 1.00 93.00 11 A 1 ATOM 95 C CB . ALA A 1 11 ? -2.914 -4.742 -0.804 1.00 92.68 11 A 1 ATOM 96 N N . SER A 1 12 ? -2.848 -2.647 -3.254 1.00 94.16 12 A 1 ATOM 97 C CA . SER A 1 12 ? -3.528 -2.024 -4.388 1.00 94.29 12 A 1 ATOM 98 C C . SER A 1 12 ? -2.657 -2.051 -5.644 1.00 94.51 12 A 1 ATOM 99 O O . SER A 1 12 ? -3.155 -2.212 -6.759 1.00 91.85 12 A 1 ATOM 100 C CB . SER A 1 12 ? -3.905 -0.586 -4.044 1.00 92.89 12 A 1 ATOM 101 O OG . SER A 1 12 ? -5.272 -0.337 -4.274 1.00 84.39 12 A 1 ATOM 102 N N . PHE A 1 13 ? -1.358 -1.907 -5.453 1.00 92.32 13 A 1 ATOM 103 C CA . PHE A 1 13 ? -0.399 -1.901 -6.551 1.00 90.93 13 A 1 ATOM 104 C C . PHE A 1 13 ? -0.107 -3.313 -7.059 1.00 92.38 13 A 1 ATOM 105 O O . PHE A 1 13 ? 0.291 -3.489 -8.210 1.00 89.62 13 A 1 ATOM 106 C CB . PHE A 1 13 ? 0.895 -1.223 -6.088 1.00 88.29 13 A 1 ATOM 107 C CG . PHE A 1 13 ? 1.650 -0.539 -7.198 1.00 84.41 13 A 1 ATOM 108 C CD1 . PHE A 1 13 ? 1.011 0.328 -8.063 1.00 81.44 13 A 1 ATOM 109 C CD2 . PHE A 1 13 ? 3.005 -0.768 -7.359 1.00 80.50 13 A 1 ATOM 110 C CE1 . PHE A 1 13 ? 1.707 0.959 -9.080 1.00 79.28 13 A 1 ATOM 111 C CE2 . PHE A 1 13 ? 3.706 -0.133 -8.375 1.00 79.73 13 A 1 ATOM 112 C CZ . PHE A 1 13 ? 3.056 0.729 -9.235 1.00 78.94 13 A 1 ATOM 113 N N . SER A 1 14 ? -0.289 -4.296 -6.216 1.00 91.01 14 A 1 ATOM 114 C CA . SER A 1 14 ? -0.025 -5.693 -6.556 1.00 90.55 14 A 1 ATOM 115 C C . SER A 1 14 ? -1.163 -6.313 -7.369 1.00 89.90 14 A 1 ATOM 116 O O . SER A 1 14 ? -0.937 -7.157 -8.238 1.00 84.14 14 A 1 ATOM 117 C CB . SER A 1 14 ? 0.221 -6.510 -5.288 1.00 86.79 14 A 1 ATOM 118 O OG . SER A 1 14 ? 1.318 -7.380 -5.454 1.00 77.26 14 A 1 ATOM 119 N N . ALA A 1 15 ? -2.403 -5.897 -7.087 1.00 87.47 15 A 1 ATOM 120 C CA . ALA A 1 15 ? -3.585 -6.438 -7.759 1.00 85.40 15 A 1 ATOM 121 C C . ALA A 1 15 ? -4.561 -5.334 -8.169 1.00 83.41 15 A 1 ATOM 122 O O . ALA A 1 15 ? -4.980 -4.553 -7.311 1.00 76.88 15 A 1 ATOM 123 C CB . ALA A 1 15 ? -4.294 -7.430 -6.850 1.00 78.37 15 A 1 ATOM 124 O OXT . ALA A 1 15 ? -4.950 -5.278 -9.340 1.00 70.30 15 A 1 #