# 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_spkb31456 # _entry.id spkb31456 # 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 ILE y ISOLEUCINE CC[C@H](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" "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 LYS 3 1 n LEU 4 1 n LEU 5 1 n ALA 6 1 n LEU 7 1 n PHE 8 1 n VAL 9 1 n ILE 10 1 n ALA 11 1 n PRO 12 1 n ILE 13 1 n LEU 14 1 n ILE 15 1 n SER 16 # _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 02:09:02)" _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 95.07 _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 91.76 1 1 A LYS 2 2 91.93 1 2 A LYS 3 2 93.19 1 3 A LEU 4 2 94.48 1 4 A LEU 5 2 94.90 1 5 A ALA 6 2 98.25 1 6 A LEU 7 2 96.62 1 7 A PHE 8 2 96.64 1 8 A VAL 9 2 97.79 1 9 A ILE 10 2 97.20 1 10 A ALA 11 2 98.24 1 11 A PRO 12 2 97.84 1 12 A ILE 13 2 96.72 1 13 A LEU 14 2 94.37 1 14 A ILE 15 2 95.35 1 15 A SER 16 2 88.10 1 16 # _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 LEU . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n ALA . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n PHE . 8 A 8 A 9 1 n VAL . 9 A 9 A 10 1 n ILE . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n PRO . 12 A 12 A 13 1 n ILE . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n ILE . 15 A 15 A 16 1 n SER . 16 A 16 # _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 ? -12.783 5.207 3.265 1.00 96.21 1 A 1 ATOM 2 C CA . MET A 1 1 ? -11.591 4.892 2.457 1.00 96.96 1 A 1 ATOM 3 C C . MET A 1 1 ? -10.441 4.409 3.337 1.00 97.14 1 A 1 ATOM 4 O O . MET A 1 1 ? -9.724 5.203 3.935 1.00 96.25 1 A 1 ATOM 5 C CB . MET A 1 1 ? -11.156 6.131 1.688 1.00 94.49 1 A 1 ATOM 6 C CG . MET A 1 1 ? -10.937 7.338 2.587 1.00 88.74 1 A 1 ATOM 7 S SD . MET A 1 1 ? -10.486 8.806 1.657 1.00 86.19 1 A 1 ATOM 8 C CE . MET A 1 1 ? -12.066 9.222 0.963 1.00 78.14 1 A 1 ATOM 9 N N . LYS A 1 2 ? -10.269 3.106 3.414 1.00 96.81 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -9.199 2.522 4.222 1.00 97.69 2 A 1 ATOM 11 C C . LYS A 1 2 ? -8.517 1.358 3.506 1.00 98.02 2 A 1 ATOM 12 O O . LYS A 1 2 ? -7.476 0.879 3.943 1.00 97.36 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -9.772 2.051 5.560 1.00 96.79 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -11.003 1.173 5.396 1.00 91.23 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -11.519 0.724 6.736 1.00 89.51 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -12.834 -0.024 6.587 1.00 83.37 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -13.946 0.818 7.029 1.00 76.61 2 A 1 ATOM 18 N N . LYS A 1 3 ? -9.108 0.903 2.401 1.00 97.75 3 A 1 ATOM 19 C CA . LYS A 1 3 ? -8.534 -0.208 1.636 1.00 98.09 3 A 1 ATOM 20 C C . LYS A 1 3 ? -7.286 0.246 0.881 1.00 98.24 3 A 1 ATOM 21 O O . LYS A 1 3 ? -6.269 -0.442 0.873 1.00 97.72 3 A 1 ATOM 22 C CB . LYS A 1 3 ? -9.567 -0.763 0.653 1.00 97.74 3 A 1 ATOM 23 C CG . LYS A 1 3 ? -10.624 -1.607 1.342 1.00 93.95 3 A 1 ATOM 24 C CD . LYS A 1 3 ? -11.554 -2.260 0.338 1.00 90.37 3 A 1 ATOM 25 C CE . LYS A 1 3 ? -12.538 -3.193 1.020 1.00 86.02 3 A 1 ATOM 26 N NZ . LYS A 1 3 ? -13.423 -3.863 0.035 1.00 78.87 3 A 1 ATOM 27 N N . LEU A 1 4 ? -7.371 1.394 0.253 1.00 97.08 4 A 1 ATOM 28 C CA . LEU A 1 4 ? -6.237 1.934 -0.492 1.00 97.53 4 A 1 ATOM 29 C C . LEU A 1 4 ? -5.109 2.318 0.458 1.00 97.83 4 A 1 ATOM 30 O O . LEU A 1 4 ? -3.933 2.216 0.116 1.00 97.44 4 A 1 ATOM 31 C CB . LEU A 1 4 ? -6.678 3.159 -1.291 1.00 97.37 4 A 1 ATOM 32 C CG . LEU A 1 4 ? -7.676 2.851 -2.400 1.00 92.80 4 A 1 ATOM 33 C CD1 . LEU A 1 4 ? -8.174 4.140 -3.026 1.00 87.96 4 A 1 ATOM 34 C CD2 . LEU A 1 4 ? -7.029 1.972 -3.464 1.00 87.87 4 A 1 ATOM 35 N N . LEU A 1 5 ? -5.470 2.755 1.643 1.00 97.92 5 A 1 ATOM 36 C CA . LEU A 1 5 ? -4.478 3.144 2.645 1.00 97.74 5 A 1 ATOM 37 C C . LEU A 1 5 ? -3.684 1.926 3.114 1.00 97.95 5 A 1 ATOM 38 O O . LEU A 1 5 ? -2.498 2.026 3.417 1.00 97.79 5 A 1 ATOM 39 C CB . LEU A 1 5 ? -5.181 3.799 3.835 1.00 97.37 5 A 1 ATOM 40 C CG . LEU A 1 5 ? -4.253 4.688 4.650 1.00 91.97 5 A 1 ATOM 41 C CD1 . LEU A 1 5 ? -3.980 5.986 3.899 1.00 89.20 5 A 1 ATOM 42 C CD2 . LEU A 1 5 ? -4.873 5.004 6.010 1.00 89.23 5 A 1 ATOM 43 N N . ALA A 1 6 ? -4.332 0.784 3.173 1.00 98.32 6 A 1 ATOM 44 C CA . ALA A 1 6 ? -3.680 -0.452 3.601 1.00 98.33 6 A 1 ATOM 45 C C . ALA A 1 6 ? -2.550 -0.833 2.648 1.00 98.44 6 A 1 ATOM 46 O O . ALA A 1 6 ? -1.435 -1.125 3.068 1.00 98.09 6 A 1 ATOM 47 C CB . ALA A 1 6 ? -4.710 -1.570 3.666 1.00 98.07 6 A 1 ATOM 48 N N . LEU A 1 7 ? -2.845 -0.824 1.356 1.00 98.37 7 A 1 ATOM 49 C CA . LEU A 1 7 ? -1.844 -1.161 0.343 1.00 98.44 7 A 1 ATOM 50 C C . LEU A 1 7 ? -0.763 -0.091 0.277 1.00 98.55 7 A 1 ATOM 51 O O . LEU A 1 7 ? 0.399 -0.388 0.004 1.00 98.28 7 A 1 ATOM 52 C CB . LEU A 1 7 ? -2.521 -1.295 -1.022 1.00 98.22 7 A 1 ATOM 53 C CG . LEU A 1 7 ? -3.422 -2.522 -1.137 1.00 95.81 7 A 1 ATOM 54 C CD1 . LEU A 1 7 ? -4.284 -2.421 -2.389 1.00 92.47 7 A 1 ATOM 55 C CD2 . LEU A 1 7 ? -2.587 -3.792 -1.187 1.00 92.85 7 A 1 ATOM 56 N N . PHE A 1 8 ? -1.149 1.138 0.527 1.00 98.53 8 A 1 ATOM 57 C CA . PHE A 1 8 ? -0.216 2.258 0.483 1.00 98.48 8 A 1 ATOM 58 C C . PHE A 1 8 ? 0.775 2.189 1.642 1.00 98.55 8 A 1 ATOM 59 O O . PHE A 1 8 ? 1.874 2.734 1.559 1.00 98.17 8 A 1 ATOM 60 C CB . PHE A 1 8 ? -0.993 3.570 0.538 1.00 98.21 8 A 1 ATOM 61 C CG . PHE A 1 8 ? -0.185 4.733 0.029 1.00 97.03 8 A 1 ATOM 62 C CD1 . PHE A 1 8 ? 0.020 4.903 -1.331 1.00 95.05 8 A 1 ATOM 63 C CD2 . PHE A 1 8 ? 0.364 5.646 0.912 1.00 95.31 8 A 1 ATOM 64 C CE1 . PHE A 1 8 ? 0.768 5.975 -1.806 1.00 94.45 8 A 1 ATOM 65 C CE2 . PHE A 1 8 ? 1.118 6.724 0.446 1.00 94.46 8 A 1 ATOM 66 C CZ . PHE A 1 8 ? 1.318 6.887 -0.915 1.00 94.80 8 A 1 ATOM 67 N N . VAL A 1 9 ? 0.396 1.516 2.707 1.00 98.59 9 A 1 ATOM 68 C CA . VAL A 1 9 ? 1.259 1.388 3.882 1.00 98.52 9 A 1 ATOM 69 C C . VAL A 1 9 ? 1.971 0.036 3.913 1.00 98.57 9 A 1 ATOM 70 O O . VAL A 1 9 ? 3.106 -0.068 4.382 1.00 98.20 9 A 1 ATOM 71 C CB . VAL A 1 9 ? 0.438 1.564 5.170 1.00 98.12 9 A 1 ATOM 72 C CG1 . VAL A 1 9 ? 1.318 1.407 6.399 1.00 96.11 9 A 1 ATOM 73 C CG2 . VAL A 1 9 ? -0.224 2.931 5.183 1.00 96.45 9 A 1 ATOM 74 N N . ILE A 1 10 ? 1.314 -0.995 3.422 1.00 98.45 10 A 1 ATOM 75 C CA . ILE A 1 10 ? 1.889 -2.337 3.418 1.00 98.35 10 A 1 ATOM 76 C C . ILE A 1 10 ? 2.856 -2.531 2.255 1.00 98.42 10 A 1 ATOM 77 O O . ILE A 1 10 ? 3.882 -3.190 2.394 1.00 98.13 10 A 1 ATOM 78 C CB . ILE A 1 10 ? 0.774 -3.396 3.349 1.00 98.05 10 A 1 ATOM 79 C CG1 . ILE A 1 10 ? -0.180 -3.240 4.538 1.00 95.97 10 A 1 ATOM 80 C CG2 . ILE A 1 10 ? 1.385 -4.793 3.348 1.00 95.84 10 A 1 ATOM 81 C CD1 . ILE A 1 10 ? 0.516 -3.413 5.880 1.00 94.40 10 A 1 ATOM 82 N N . ALA A 1 11 ? 2.516 -1.974 1.105 1.00 98.44 11 A 1 ATOM 83 C CA . ALA A 1 11 ? 3.352 -2.110 -0.089 1.00 98.40 11 A 1 ATOM 84 C C . ALA A 1 11 ? 4.792 -1.647 0.154 1.00 98.47 11 A 1 ATOM 85 O O . ALA A 1 11 ? 5.733 -2.399 -0.099 1.00 97.88 11 A 1 ATOM 86 C CB . ALA A 1 11 ? 2.725 -1.346 -1.249 1.00 98.02 11 A 1 ATOM 87 N N . PRO A 1 12 ? 4.990 -0.429 0.628 1.00 98.36 12 A 1 ATOM 88 C CA . PRO A 1 12 ? 6.338 0.094 0.880 1.00 98.20 12 A 1 ATOM 89 C C . PRO A 1 12 ? 7.088 -0.694 1.949 1.00 98.29 12 A 1 ATOM 90 O O . PRO A 1 12 ? 8.309 -0.798 1.909 1.00 97.65 12 A 1 ATOM 91 C CB . PRO A 1 12 ? 6.084 1.536 1.330 1.00 97.55 12 A 1 ATOM 92 C CG . PRO A 1 12 ? 4.686 1.537 1.835 1.00 96.69 12 A 1 ATOM 93 C CD . PRO A 1 12 ? 3.954 0.550 0.966 1.00 98.11 12 A 1 ATOM 94 N N . ILE A 1 13 ? 6.382 -1.243 2.896 1.00 97.88 13 A 1 ATOM 95 C CA . ILE A 1 13 ? 6.996 -2.017 3.976 1.00 97.96 13 A 1 ATOM 96 C C . ILE A 1 13 ? 7.478 -3.374 3.469 1.00 98.06 13 A 1 ATOM 97 O O . ILE A 1 13 ? 8.469 -3.915 3.956 1.00 97.19 13 A 1 ATOM 98 C CB . ILE A 1 13 ? 5.995 -2.218 5.131 1.00 97.61 13 A 1 ATOM 99 C CG1 . ILE A 1 13 ? 5.605 -0.865 5.730 1.00 95.84 13 A 1 ATOM 100 C CG2 . ILE A 1 13 ? 6.612 -3.104 6.214 1.00 95.43 13 A 1 ATOM 101 C CD1 . ILE A 1 13 ? 4.489 -0.978 6.757 1.00 93.75 13 A 1 ATOM 102 N N . LEU A 1 14 ? 6.782 -3.922 2.489 1.00 96.83 14 A 1 ATOM 103 C CA . LEU A 1 14 ? 7.135 -5.229 1.937 1.00 96.82 14 A 1 ATOM 104 C C . LEU A 1 14 ? 8.410 -5.152 1.106 1.00 96.82 14 A 1 ATOM 105 O O . LEU A 1 14 ? 9.243 -6.057 1.148 1.00 95.55 14 A 1 ATOM 106 C CB . LEU A 1 14 ? 5.984 -5.750 1.068 1.00 96.32 14 A 1 ATOM 107 C CG . LEU A 1 14 ? 4.721 -6.082 1.853 1.00 93.30 14 A 1 ATOM 108 C CD1 . LEU A 1 14 ? 3.583 -6.411 0.895 1.00 90.02 14 A 1 ATOM 109 C CD2 . LEU A 1 14 ? 4.971 -7.266 2.780 1.00 89.29 14 A 1 ATOM 110 N N . ILE A 1 15 ? 8.561 -4.099 0.345 1.00 97.27 15 A 1 ATOM 111 C CA . ILE A 1 15 ? 9.730 -3.920 -0.510 1.00 97.36 15 A 1 ATOM 112 C C . ILE A 1 15 ? 10.922 -3.337 0.245 1.00 97.46 15 A 1 ATOM 113 O O . ILE A 1 15 ? 12.033 -3.309 -0.270 1.00 96.59 15 A 1 ATOM 114 C CB . ILE A 1 15 ? 9.389 -2.997 -1.690 1.00 96.79 15 A 1 ATOM 115 C CG1 . ILE A 1 15 ? 8.932 -1.629 -1.184 1.00 94.12 15 A 1 ATOM 116 C CG2 . ILE A 1 15 ? 8.309 -3.633 -2.545 1.00 93.40 15 A 1 ATOM 117 C CD1 . ILE A 1 15 ? 8.838 -0.587 -2.282 1.00 89.80 15 A 1 ATOM 118 N N . SER A 1 16 ? 10.682 -2.890 1.446 1.00 94.81 16 A 1 ATOM 119 C CA . SER A 1 16 ? 11.745 -2.278 2.243 1.00 93.13 16 A 1 ATOM 120 C C . SER A 1 16 ? 11.763 -2.818 3.669 1.00 89.65 16 A 1 ATOM 121 O O . SER A 1 16 ? 12.655 -2.434 4.445 1.00 84.74 16 A 1 ATOM 122 C CB . SER A 1 16 ? 11.575 -0.756 2.261 1.00 89.60 16 A 1 ATOM 123 O OG . SER A 1 16 ? 12.708 -0.140 2.832 1.00 81.65 16 A 1 ATOM 124 O OXT . SER A 1 16 ? 10.878 -3.612 4.018 1.00 83.11 16 A 1 #