# 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_spkb31358 # _entry.id spkb31358 # 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" "C3 H7 N O3" 105.093 SER y SERINE C([C@@H](C(=O)O)N)O ? "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 LYS 2 1 n LEU 3 1 n SER 4 1 n ALA 5 1 n LEU 6 1 n VAL 7 1 n PHE 8 1 n VAL 9 1 n ALA 10 1 n SER 11 1 n VAL 12 1 n MET 13 1 n LEU 14 1 n VAL 15 1 n ALA 16 1 n ALA 17 # _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 @ 2025-07-13 10:10:09)" _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 95.53 _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 87.93 1 1 A LYS 2 2 89.41 1 2 A LEU 3 2 94.04 1 3 A SER 4 2 96.58 1 4 A ALA 5 2 98.28 1 5 A LEU 6 2 96.30 1 6 A VAL 7 2 97.90 1 7 A PHE 8 2 96.86 1 8 A VAL 9 2 97.93 1 9 A ALA 10 2 98.19 1 10 A SER 11 2 97.15 1 11 A VAL 12 2 97.81 1 12 A MET 13 2 94.70 1 13 A LEU 14 2 95.87 1 14 A VAL 15 2 97.53 1 15 A ALA 16 2 98.11 1 16 A ALA 17 2 94.21 1 17 # _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 LEU . 3 A 3 A 4 1 n SER . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n VAL . 7 A 7 A 8 1 n PHE . 8 A 8 A 9 1 n VAL . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n SER . 11 A 11 A 12 1 n VAL . 12 A 12 A 13 1 n MET . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n VAL . 15 A 15 A 16 1 n ALA . 16 A 16 A 17 1 n ALA . 17 A 17 # _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 ? -14.500 0.195 1.978 1.00 93.29 1 A 1 ATOM 2 C CA . MET A 1 1 ? -13.057 0.355 1.746 1.00 94.12 1 A 1 ATOM 3 C C . MET A 1 1 ? -12.542 -0.716 0.793 1.00 94.62 1 A 1 ATOM 4 O O . MET A 1 1 ? -13.090 -1.814 0.732 1.00 91.73 1 A 1 ATOM 5 C CB . MET A 1 1 ? -12.287 0.250 3.059 1.00 90.20 1 A 1 ATOM 6 C CG . MET A 1 1 ? -12.723 1.278 4.082 1.00 86.26 1 A 1 ATOM 7 S SD . MET A 1 1 ? -11.866 1.089 5.652 1.00 81.80 1 A 1 ATOM 8 C CE . MET A 1 1 ? -12.714 2.316 6.620 1.00 71.39 1 A 1 ATOM 9 N N . LYS A 1 2 ? -11.494 -0.415 0.063 1.00 95.29 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -10.919 -1.364 -0.883 1.00 96.00 2 A 1 ATOM 11 C C . LYS A 1 2 ? -9.560 -1.846 -0.376 1.00 96.43 2 A 1 ATOM 12 O O . LYS A 1 2 ? -8.620 -1.057 -0.270 1.00 95.84 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -10.776 -0.711 -2.255 1.00 94.19 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -12.111 -0.308 -2.862 1.00 88.48 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -11.919 0.307 -4.235 1.00 85.47 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -13.245 0.777 -4.808 1.00 79.13 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -14.191 -0.354 -5.007 1.00 73.83 2 A 1 ATOM 18 N N . LEU A 1 3 ? -9.460 -3.128 -0.074 1.00 96.27 3 A 1 ATOM 19 C CA . LEU A 1 3 ? -8.220 -3.717 0.422 1.00 97.31 3 A 1 ATOM 20 C C . LEU A 1 3 ? -7.109 -3.602 -0.616 1.00 97.95 3 A 1 ATOM 21 O O . LEU A 1 3 ? -5.953 -3.340 -0.275 1.00 97.50 3 A 1 ATOM 22 C CB . LEU A 1 3 ? -8.454 -5.187 0.775 1.00 96.64 3 A 1 ATOM 23 C CG . LEU A 1 3 ? -9.438 -5.401 1.924 1.00 92.09 3 A 1 ATOM 24 C CD1 . LEU A 1 3 ? -9.739 -6.883 2.081 1.00 88.13 3 A 1 ATOM 25 C CD2 . LEU A 1 3 ? -8.879 -4.830 3.220 1.00 86.44 3 A 1 ATOM 26 N N . SER A 1 4 ? -7.463 -3.785 -1.882 1.00 97.80 4 A 1 ATOM 27 C CA . SER A 1 4 ? -6.498 -3.691 -2.975 1.00 98.07 4 A 1 ATOM 28 C C . SER A 1 4 ? -5.874 -2.301 -3.039 1.00 98.27 4 A 1 ATOM 29 O O . SER A 1 4 ? -4.675 -2.153 -3.281 1.00 98.02 4 A 1 ATOM 30 C CB . SER A 1 4 ? -7.171 -4.010 -4.304 1.00 97.43 4 A 1 ATOM 31 O OG . SER A 1 4 ? -6.232 -3.936 -5.350 1.00 89.92 4 A 1 ATOM 32 N N . ALA A 1 5 ? -6.692 -1.277 -2.818 1.00 98.14 5 A 1 ATOM 33 C CA . ALA A 1 5 ? -6.223 0.105 -2.849 1.00 98.37 5 A 1 ATOM 34 C C . ALA A 1 5 ? -5.222 0.363 -1.725 1.00 98.54 5 A 1 ATOM 35 O O . ALA A 1 5 ? -4.225 1.057 -1.916 1.00 98.26 5 A 1 ATOM 36 C CB . ALA A 1 5 ? -7.407 1.059 -2.726 1.00 98.08 5 A 1 ATOM 37 N N . LEU A 1 6 ? -5.495 -0.192 -0.546 1.00 98.34 6 A 1 ATOM 38 C CA . LEU A 1 6 ? -4.618 -0.021 0.605 1.00 98.37 6 A 1 ATOM 39 C C . LEU A 1 6 ? -3.254 -0.647 0.345 1.00 98.56 6 A 1 ATOM 40 O O . LEU A 1 6 ? -2.224 -0.099 0.742 1.00 98.50 6 A 1 ATOM 41 C CB . LEU A 1 6 ? -5.255 -0.654 1.845 1.00 98.21 6 A 1 ATOM 42 C CG . LEU A 1 6 ? -6.516 0.054 2.335 1.00 93.93 6 A 1 ATOM 43 C CD1 . LEU A 1 6 ? -7.180 -0.765 3.437 1.00 91.77 6 A 1 ATOM 44 C CD2 . LEU A 1 6 ? -6.187 1.449 2.840 1.00 92.76 6 A 1 ATOM 45 N N . VAL A 1 7 ? -3.248 -1.784 -0.315 1.00 98.30 7 A 1 ATOM 46 C CA . VAL A 1 7 ? -2.008 -2.485 -0.637 1.00 98.42 7 A 1 ATOM 47 C C . VAL A 1 7 ? -1.149 -1.649 -1.581 1.00 98.53 7 A 1 ATOM 48 O O . VAL A 1 7 ? 0.074 -1.575 -1.431 1.00 98.40 7 A 1 ATOM 49 C CB . VAL A 1 7 ? -2.299 -3.851 -1.275 1.00 98.17 7 A 1 ATOM 50 C CG1 . VAL A 1 7 ? -1.002 -4.537 -1.686 1.00 96.94 7 A 1 ATOM 51 C CG2 . VAL A 1 7 ? -3.074 -4.724 -0.300 1.00 96.54 7 A 1 ATOM 52 N N . PHE A 1 8 ? -1.794 -1.014 -2.554 1.00 98.25 8 A 1 ATOM 53 C CA . PHE A 1 8 ? -1.089 -0.171 -3.518 1.00 98.31 8 A 1 ATOM 54 C C . PHE A 1 8 ? -0.421 1.006 -2.824 1.00 98.45 8 A 1 ATOM 55 O O . PHE A 1 8 ? 0.748 1.305 -3.066 1.00 98.25 8 A 1 ATOM 56 C CB . PHE A 1 8 ? -2.063 0.338 -4.583 1.00 98.16 8 A 1 ATOM 57 C CG . PHE A 1 8 ? -1.955 -0.429 -5.879 1.00 97.13 8 A 1 ATOM 58 C CD1 . PHE A 1 8 ? -2.418 -1.730 -5.967 1.00 95.67 8 A 1 ATOM 59 C CD2 . PHE A 1 8 ? -1.385 0.160 -6.994 1.00 95.95 8 A 1 ATOM 60 C CE1 . PHE A 1 8 ? -2.311 -2.442 -7.150 1.00 95.19 8 A 1 ATOM 61 C CE2 . PHE A 1 8 ? -1.279 -0.543 -8.185 1.00 94.99 8 A 1 ATOM 62 C CZ . PHE A 1 8 ? -1.740 -1.847 -8.266 1.00 95.10 8 A 1 ATOM 63 N N . VAL A 1 9 ? -1.171 1.675 -1.940 1.00 98.45 9 A 1 ATOM 64 C CA . VAL A 1 9 ? -0.647 2.819 -1.202 1.00 98.42 9 A 1 ATOM 65 C C . VAL A 1 9 ? 0.519 2.393 -0.316 1.00 98.52 9 A 1 ATOM 66 O O . VAL A 1 9 ? 1.542 3.079 -0.236 1.00 98.35 9 A 1 ATOM 67 C CB . VAL A 1 9 ? -1.742 3.472 -0.340 1.00 98.11 9 A 1 ATOM 68 C CG1 . VAL A 1 9 ? -1.168 4.616 0.483 1.00 96.84 9 A 1 ATOM 69 C CG2 . VAL A 1 9 ? -2.874 3.973 -1.225 1.00 96.81 9 A 1 ATOM 70 N N . ALA A 1 10 ? 0.356 1.265 0.353 1.00 98.25 10 A 1 ATOM 71 C CA . ALA A 1 10 ? 1.394 0.750 1.241 1.00 98.25 10 A 1 ATOM 72 C C . ALA A 1 10 ? 2.670 0.426 0.468 1.00 98.42 10 A 1 ATOM 73 O O . ALA A 1 10 ? 3.778 0.659 0.958 1.00 98.07 10 A 1 ATOM 74 C CB . ALA A 1 10 ? 0.886 -0.497 1.952 1.00 97.94 10 A 1 ATOM 75 N N . SER A 1 11 ? 2.516 -0.098 -0.733 1.00 98.42 11 A 1 ATOM 76 C CA . SER A 1 11 ? 3.654 -0.450 -1.575 1.00 98.45 11 A 1 ATOM 77 C C . SER A 1 11 ? 4.457 0.788 -1.959 1.00 98.60 11 A 1 ATOM 78 O O . SER A 1 11 ? 5.689 0.774 -1.938 1.00 98.28 11 A 1 ATOM 79 C CB . SER A 1 11 ? 3.178 -1.166 -2.839 1.00 98.11 11 A 1 ATOM 80 O OG . SER A 1 11 ? 4.283 -1.546 -3.631 1.00 91.05 11 A 1 ATOM 81 N N . VAL A 1 12 ? 3.750 1.864 -2.311 1.00 98.52 12 A 1 ATOM 82 C CA . VAL A 1 12 ? 4.398 3.115 -2.701 1.00 98.51 12 A 1 ATOM 83 C C . VAL A 1 12 ? 5.160 3.713 -1.524 1.00 98.63 12 A 1 ATOM 84 O O . VAL A 1 12 ? 6.304 4.156 -1.663 1.00 98.27 12 A 1 ATOM 85 C CB . VAL A 1 12 ? 3.370 4.132 -3.223 1.00 98.11 12 A 1 ATOM 86 C CG1 . VAL A 1 12 ? 4.044 5.466 -3.532 1.00 96.32 12 A 1 ATOM 87 C CG2 . VAL A 1 12 ? 2.680 3.590 -4.465 1.00 96.29 12 A 1 ATOM 88 N N . MET A 1 13 ? 4.509 3.742 -0.366 1.00 98.50 13 A 1 ATOM 89 C CA . MET A 1 13 ? 5.121 4.297 0.837 1.00 98.49 13 A 1 ATOM 90 C C . MET A 1 13 ? 6.315 3.463 1.281 1.00 98.57 13 A 1 ATOM 91 O O . MET A 1 13 ? 7.289 3.995 1.814 1.00 98.13 13 A 1 ATOM 92 C CB . MET A 1 13 ? 4.089 4.375 1.961 1.00 98.26 13 A 1 ATOM 93 C CG . MET A 1 13 ? 3.000 5.394 1.680 1.00 95.59 13 A 1 ATOM 94 S SD . MET A 1 13 ? 3.601 7.079 1.677 1.00 89.48 13 A 1 ATOM 95 C CE . MET A 1 13 ? 3.925 7.317 3.420 1.00 80.57 13 A 1 ATOM 96 N N . LEU A 1 14 ? 6.241 2.163 1.063 1.00 98.47 14 A 1 ATOM 97 C CA . LEU A 1 14 ? 7.320 1.252 1.438 1.00 98.42 14 A 1 ATOM 98 C C . LEU A 1 14 ? 8.608 1.600 0.704 1.00 98.57 14 A 1 ATOM 99 O O . LEU A 1 14 ? 9.692 1.603 1.295 1.00 98.29 14 A 1 ATOM 100 C CB . LEU A 1 14 ? 6.924 -0.191 1.118 1.00 98.15 14 A 1 ATOM 101 C CG . LEU A 1 14 ? 7.971 -1.227 1.529 1.00 92.72 14 A 1 ATOM 102 C CD1 . LEU A 1 14 ? 8.126 -1.264 3.040 1.00 90.85 14 A 1 ATOM 103 C CD2 . LEU A 1 14 ? 7.583 -2.599 1.003 1.00 91.51 14 A 1 ATOM 104 N N . VAL A 1 15 ? 8.495 1.887 -0.585 1.00 98.54 15 A 1 ATOM 105 C CA . VAL A 1 15 ? 9.650 2.243 -1.402 1.00 98.43 15 A 1 ATOM 106 C C . VAL A 1 15 ? 10.185 3.616 -1.024 1.00 98.54 15 A 1 ATOM 107 O O . VAL A 1 15 ? 11.402 3.834 -0.980 1.00 98.10 15 A 1 ATOM 108 C CB . VAL A 1 15 ? 9.287 2.226 -2.898 1.00 97.83 15 A 1 ATOM 109 C CG1 . VAL A 1 15 ? 10.487 2.644 -3.740 1.00 95.42 15 A 1 ATOM 110 C CG2 . VAL A 1 15 ? 8.804 0.849 -3.309 1.00 95.87 15 A 1 ATOM 111 N N . ALA A 1 16 ? 9.267 4.546 -0.768 1.00 98.38 16 A 1 ATOM 112 C CA . ALA A 1 16 ? 9.638 5.909 -0.407 1.00 98.27 16 A 1 ATOM 113 C C . ALA A 1 16 ? 10.186 5.992 1.012 1.00 98.39 16 A 1 ATOM 114 O O . ALA A 1 16 ? 11.009 6.859 1.317 1.00 97.87 16 A 1 ATOM 115 C CB . ALA A 1 16 ? 8.427 6.831 -0.553 1.00 97.66 16 A 1 ATOM 116 N N . ALA A 1 17 ? 9.720 5.097 1.882 1.00 97.57 17 A 1 ATOM 117 C CA . ALA A 1 17 ? 10.127 5.074 3.285 1.00 96.82 17 A 1 ATOM 118 C C . ALA A 1 17 ? 11.631 4.863 3.408 1.00 95.72 17 A 1 ATOM 119 O O . ALA A 1 17 ? 12.274 5.590 4.189 1.00 92.89 17 A 1 ATOM 120 C CB . ALA A 1 17 ? 9.366 3.985 4.039 1.00 95.04 17 A 1 ATOM 121 O OXT . ALA A 1 17 ? 12.157 3.971 2.749 1.00 87.25 17 A 1 #