# 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_spkb22756 # _entry.id spkb22756 # 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" "C4 H7 N O4" 133.103 ASP y "ASPARTIC ACID" C([C@@H](C(=O)O)N)C(=O)O ? "L-PEPTIDE LINKING" "C6 H10 N3 O2" 156.162 HIS y HISTIDINE c1c([nH+]c[nH]1)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" "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 VAL 2 1 n TRP 3 1 n ASP 4 1 n PHE 5 1 n VAL 6 1 n LEU 7 1 n SER 8 1 n LEU 9 1 n PHE 10 1 n HIS 11 1 n SER 12 1 n LEU 13 1 n LEU 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 09:46:27)" _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 94.80 _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 87.68 1 1 A VAL 2 2 93.60 1 2 A TRP 3 2 95.36 1 3 A ASP 4 2 95.44 1 4 A PHE 5 2 95.89 1 5 A VAL 6 2 97.71 1 6 A LEU 7 2 96.15 1 7 A SER 8 2 96.48 1 8 A LEU 9 2 97.09 1 9 A PHE 10 2 95.02 1 10 A HIS 11 2 94.12 1 11 A SER 12 2 97.20 1 12 A LEU 13 2 96.44 1 13 A LEU 14 2 95.95 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 VAL . 2 A 2 A 3 1 n TRP . 3 A 3 A 4 1 n ASP . 4 A 4 A 5 1 n PHE . 5 A 5 A 6 1 n VAL . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n SER . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n PHE . 10 A 10 A 11 1 n HIS . 11 A 11 A 12 1 n SER . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n LEU . 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 ? 7.876 -5.277 0.595 1.00 91.61 1 A 1 ATOM 2 C CA . MET A 1 1 ? 7.735 -5.656 2.011 1.00 93.60 1 A 1 ATOM 3 C C . MET A 1 1 ? 6.254 -5.773 2.375 1.00 94.44 1 A 1 ATOM 4 O O . MET A 1 1 ? 5.387 -5.480 1.562 1.00 93.21 1 A 1 ATOM 5 C CB . MET A 1 1 ? 8.403 -4.606 2.901 1.00 90.19 1 A 1 ATOM 6 C CG . MET A 1 1 ? 9.920 -4.717 2.888 1.00 83.91 1 A 1 ATOM 7 S SD . MET A 1 1 ? 10.694 -3.353 3.748 1.00 81.38 1 A 1 ATOM 8 C CE . MET A 1 1 ? 12.409 -3.819 3.585 1.00 73.08 1 A 1 ATOM 9 N N . VAL A 1 2 ? 5.995 -6.198 3.610 1.00 93.32 2 A 1 ATOM 10 C CA . VAL A 1 2 ? 4.619 -6.381 4.080 1.00 95.94 2 A 1 ATOM 11 C C . VAL A 1 2 ? 3.864 -5.055 4.092 1.00 97.23 2 A 1 ATOM 12 O O . VAL A 1 2 ? 2.682 -4.990 3.732 1.00 96.83 2 A 1 ATOM 13 C CB . VAL A 1 2 ? 4.589 -6.974 5.506 1.00 93.95 2 A 1 ATOM 14 C CG1 . VAL A 1 2 ? 3.373 -7.863 5.670 1.00 88.98 2 A 1 ATOM 15 C CG2 . VAL A 1 2 ? 5.860 -7.743 5.826 1.00 88.92 2 A 1 ATOM 16 N N . TRP A 1 3 ? 4.545 -4.021 4.514 1.00 96.48 3 A 1 ATOM 17 C CA . TRP A 1 3 ? 3.922 -2.699 4.574 1.00 97.27 3 A 1 ATOM 18 C C . TRP A 1 3 ? 3.539 -2.207 3.187 1.00 97.71 3 A 1 ATOM 19 O O . TRP A 1 3 ? 2.549 -1.499 3.018 1.00 97.47 3 A 1 ATOM 20 C CB . TRP A 1 3 ? 4.886 -1.717 5.239 1.00 96.88 3 A 1 ATOM 21 C CG . TRP A 1 3 ? 4.353 -0.328 5.225 1.00 95.91 3 A 1 ATOM 22 C CD1 . TRP A 1 3 ? 4.966 0.758 4.687 1.00 94.57 3 A 1 ATOM 23 C CD2 . TRP A 1 3 ? 3.093 0.133 5.744 1.00 95.86 3 A 1 ATOM 24 N NE1 . TRP A 1 3 ? 4.166 1.864 4.845 1.00 94.24 3 A 1 ATOM 25 C CE2 . TRP A 1 3 ? 3.014 1.516 5.484 1.00 95.13 3 A 1 ATOM 26 C CE3 . TRP A 1 3 ? 2.032 -0.492 6.401 1.00 94.89 3 A 1 ATOM 27 C CZ2 . TRP A 1 3 ? 1.899 2.272 5.869 1.00 94.10 3 A 1 ATOM 28 C CZ3 . TRP A 1 3 ? 0.924 0.268 6.781 1.00 92.39 3 A 1 ATOM 29 C CH2 . TRP A 1 3 ? 0.870 1.633 6.516 1.00 92.19 3 A 1 ATOM 30 N N . ASP A 1 4 ? 4.314 -2.582 2.200 1.00 97.61 4 A 1 ATOM 31 C CA . ASP A 1 4 ? 4.037 -2.192 0.816 1.00 97.82 4 A 1 ATOM 32 C C . ASP A 1 4 ? 2.667 -2.704 0.395 1.00 98.12 4 A 1 ATOM 33 O O . ASP A 1 4 ? 1.965 -2.062 -0.387 1.00 97.77 4 A 1 ATOM 34 C CB . ASP A 1 4 ? 5.114 -2.768 -0.103 1.00 97.09 4 A 1 ATOM 35 C CG . ASP A 1 4 ? 6.481 -2.229 0.254 1.00 94.01 4 A 1 ATOM 36 O OD1 . ASP A 1 4 ? 7.044 -2.685 1.254 1.00 90.87 4 A 1 ATOM 37 O OD2 . ASP A 1 4 ? 6.983 -1.355 -0.473 1.00 90.22 4 A 1 ATOM 38 N N . PHE A 1 5 ? 2.296 -3.840 0.919 1.00 97.14 5 A 1 ATOM 39 C CA . PHE A 1 5 ? 1.003 -4.444 0.619 1.00 97.45 5 A 1 ATOM 40 C C . PHE A 1 5 ? -0.136 -3.558 1.118 1.00 98.00 5 A 1 ATOM 41 O O . PHE A 1 5 ? -1.100 -3.300 0.400 1.00 97.83 5 A 1 ATOM 42 C CB . PHE A 1 5 ? 0.940 -5.823 1.284 1.00 97.26 5 A 1 ATOM 43 C CG . PHE A 1 5 ? -0.469 -6.288 1.498 1.00 96.44 5 A 1 ATOM 44 C CD1 . PHE A 1 5 ? -1.256 -6.643 0.420 1.00 94.63 5 A 1 ATOM 45 C CD2 . PHE A 1 5 ? -0.997 -6.353 2.772 1.00 94.68 5 A 1 ATOM 46 C CE1 . PHE A 1 5 ? -2.561 -7.069 0.605 1.00 93.72 5 A 1 ATOM 47 C CE2 . PHE A 1 5 ? -2.306 -6.775 2.967 1.00 93.68 5 A 1 ATOM 48 C CZ . PHE A 1 5 ? -3.086 -7.132 1.883 1.00 93.99 5 A 1 ATOM 49 N N . VAL A 1 6 ? -0.014 -3.110 2.356 1.00 97.99 6 A 1 ATOM 50 C CA . VAL A 1 6 ? -1.029 -2.246 2.961 1.00 98.13 6 A 1 ATOM 51 C C . VAL A 1 6 ? -1.095 -0.916 2.228 1.00 98.32 6 A 1 ATOM 52 O O . VAL A 1 6 ? -2.177 -0.378 1.989 1.00 98.24 6 A 1 ATOM 53 C CB . VAL A 1 6 ? -0.724 -1.996 4.451 1.00 97.88 6 A 1 ATOM 54 C CG1 . VAL A 1 6 ? -1.869 -1.240 5.106 1.00 96.75 6 A 1 ATOM 55 C CG2 . VAL A 1 6 ? -0.456 -3.299 5.174 1.00 96.67 6 A 1 ATOM 56 N N . LEU A 1 7 ? 0.057 -0.398 1.884 1.00 97.81 7 A 1 ATOM 57 C CA . LEU A 1 7 ? 0.142 0.881 1.189 1.00 97.70 7 A 1 ATOM 58 C C . LEU A 1 7 ? -0.550 0.802 -0.168 1.00 97.87 7 A 1 ATOM 59 O O . LEU A 1 7 ? -1.308 1.691 -0.548 1.00 97.90 7 A 1 ATOM 60 C CB . LEU A 1 7 ? 1.613 1.273 1.015 1.00 97.37 7 A 1 ATOM 61 C CG . LEU A 1 7 ? 1.868 2.764 1.201 1.00 94.23 7 A 1 ATOM 62 C CD1 . LEU A 1 7 ? 1.574 3.181 2.633 1.00 93.25 7 A 1 ATOM 63 C CD2 . LEU A 1 7 ? 3.315 3.080 0.846 1.00 93.06 7 A 1 ATOM 64 N N . SER A 1 8 ? -0.292 -0.257 -0.876 1.00 97.88 8 A 1 ATOM 65 C CA . SER A 1 8 ? -0.897 -0.471 -2.186 1.00 97.97 8 A 1 ATOM 66 C C . SER A 1 8 ? -2.406 -0.625 -2.069 1.00 98.22 8 A 1 ATOM 67 O O . SER A 1 8 ? -3.165 -0.100 -2.885 1.00 97.82 8 A 1 ATOM 68 C CB . SER A 1 8 ? -0.292 -1.711 -2.826 1.00 97.51 8 A 1 ATOM 69 O OG . SER A 1 8 ? -0.647 -1.765 -4.192 1.00 89.47 8 A 1 ATOM 70 N N . LEU A 1 9 ? -2.832 -1.333 -1.055 1.00 98.09 9 A 1 ATOM 71 C CA . LEU A 1 9 ? -4.254 -1.552 -0.811 1.00 98.10 9 A 1 ATOM 72 C C . LEU A 1 9 ? -4.961 -0.237 -0.509 1.00 98.19 9 A 1 ATOM 73 O O . LEU A 1 9 ? -6.020 0.053 -1.063 1.00 98.01 9 A 1 ATOM 74 C CB . LEU A 1 9 ? -4.419 -2.513 0.364 1.00 98.00 9 A 1 ATOM 75 C CG . LEU A 1 9 ? -5.869 -2.865 0.656 1.00 96.67 9 A 1 ATOM 76 C CD1 . LEU A 1 9 ? -6.345 -3.940 -0.317 1.00 94.91 9 A 1 ATOM 77 C CD2 . LEU A 1 9 ? -6.008 -3.351 2.084 1.00 94.75 9 A 1 ATOM 78 N N . PHE A 1 10 ? -4.372 0.549 0.369 1.00 97.94 10 A 1 ATOM 79 C CA . PHE A 1 10 ? -4.935 1.841 0.752 1.00 97.69 10 A 1 ATOM 80 C C . PHE A 1 10 ? -5.025 2.770 -0.452 1.00 97.86 10 A 1 ATOM 81 O O . PHE A 1 10 ? -6.021 3.463 -0.643 1.00 97.63 10 A 1 ATOM 82 C CB . PHE A 1 10 ? -4.057 2.470 1.831 1.00 97.31 10 A 1 ATOM 83 C CG . PHE A 1 10 ? -4.661 3.720 2.409 1.00 95.30 10 A 1 ATOM 84 C CD1 . PHE A 1 10 ? -5.684 3.642 3.333 1.00 92.06 10 A 1 ATOM 85 C CD2 . PHE A 1 10 ? -4.203 4.963 2.012 1.00 92.60 10 A 1 ATOM 86 C CE1 . PHE A 1 10 ? -6.247 4.789 3.863 1.00 92.26 10 A 1 ATOM 87 C CE2 . PHE A 1 10 ? -4.770 6.119 2.535 1.00 92.12 10 A 1 ATOM 88 C CZ . PHE A 1 10 ? -5.790 6.029 3.462 1.00 92.40 10 A 1 ATOM 89 N N . HIS A 1 11 ? -3.982 2.782 -1.265 1.00 98.00 11 A 1 ATOM 90 C CA . HIS A 1 11 ? -3.951 3.633 -2.450 1.00 97.94 11 A 1 ATOM 91 C C . HIS A 1 11 ? -5.019 3.204 -3.452 1.00 98.19 11 A 1 ATOM 92 O O . HIS A 1 11 ? -5.633 4.039 -4.110 1.00 97.70 11 A 1 ATOM 93 C CB . HIS A 1 11 ? -2.567 3.568 -3.095 1.00 97.00 11 A 1 ATOM 94 C CG . HIS A 1 11 ? -1.969 4.932 -3.283 1.00 94.95 11 A 1 ATOM 95 N ND1 . HIS A 1 11 ? -2.396 5.800 -4.249 1.00 88.52 11 A 1 ATOM 96 C CD2 . HIS A 1 11 ? -0.973 5.550 -2.614 1.00 89.07 11 A 1 ATOM 97 C CE1 . HIS A 1 11 ? -1.685 6.916 -4.167 1.00 89.21 11 A 1 ATOM 98 N NE2 . HIS A 1 11 ? -0.807 6.793 -3.184 1.00 90.63 11 A 1 ATOM 99 N N . SER A 1 12 ? -5.243 1.920 -3.557 1.00 98.30 12 A 1 ATOM 100 C CA . SER A 1 12 ? -6.254 1.387 -4.463 1.00 98.25 12 A 1 ATOM 101 C C . SER A 1 12 ? -7.651 1.775 -3.999 1.00 98.38 12 A 1 ATOM 102 O O . SER A 1 12 ? -8.525 2.071 -4.809 1.00 97.51 12 A 1 ATOM 103 C CB . SER A 1 12 ? -6.143 -0.128 -4.535 1.00 97.61 12 A 1 ATOM 104 O OG . SER A 1 12 ? -5.688 -0.522 -5.811 1.00 93.12 12 A 1 ATOM 105 N N . LEU A 1 13 ? -7.853 1.772 -2.696 1.00 97.91 13 A 1 ATOM 106 C CA . LEU A 1 13 ? -9.143 2.136 -2.115 1.00 97.72 13 A 1 ATOM 107 C C . LEU A 1 13 ? -9.433 3.613 -2.331 1.00 97.84 13 A 1 ATOM 108 O O . LEU A 1 13 ? -10.570 4.002 -2.609 1.00 97.22 13 A 1 ATOM 109 C CB . LEU A 1 13 ? -9.143 1.808 -0.621 1.00 97.32 13 A 1 ATOM 110 C CG . LEU A 1 13 ? -10.487 2.057 0.053 1.00 95.97 13 A 1 ATOM 111 C CD1 . LEU A 1 13 ? -10.832 0.908 0.981 1.00 94.06 13 A 1 ATOM 112 C CD2 . LEU A 1 13 ? -10.452 3.361 0.827 1.00 93.45 13 A 1 ATOM 113 N N . LEU A 1 14 ? -8.412 4.432 -2.195 1.00 97.65 14 A 1 ATOM 114 C CA . LEU A 1 14 ? -8.546 5.872 -2.378 1.00 97.37 14 A 1 ATOM 115 C C . LEU A 1 14 ? -8.925 6.207 -3.813 1.00 97.16 14 A 1 ATOM 116 O O . LEU A 1 14 ? -9.733 7.108 -4.059 1.00 96.39 14 A 1 ATOM 117 C CB . LEU A 1 14 ? -7.229 6.562 -2.010 1.00 96.73 14 A 1 ATOM 118 C CG . LEU A 1 14 ? -7.328 8.082 -1.948 1.00 95.65 14 A 1 ATOM 119 C CD1 . LEU A 1 14 ? -7.925 8.522 -0.617 1.00 93.96 14 A 1 ATOM 120 C CD2 . LEU A 1 14 ? -5.950 8.701 -2.130 1.00 92.70 14 A 1 ATOM 121 N N . ALA A 1 15 ? -8.353 5.504 -4.739 1.00 94.41 15 A 1 ATOM 122 C CA . ALA A 1 15 ? -8.606 5.733 -6.160 1.00 91.35 15 A 1 ATOM 123 C C . ALA A 1 15 ? -9.673 4.778 -6.670 1.00 86.60 15 A 1 ATOM 124 O O . ALA A 1 15 ? -10.713 5.250 -7.174 1.00 81.72 15 A 1 ATOM 125 C CB . ALA A 1 15 ? -7.300 5.557 -6.947 1.00 85.85 15 A 1 ATOM 126 O OXT . ALA A 1 15 ? -9.475 3.569 -6.553 1.00 77.43 15 A 1 #