# 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_spkb39860 # _entry.id spkb39860 # 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" "C3 H7 N O3" 105.093 SER y SERINE C([C@@H](C(=O)O)N)O ? "L-PEPTIDE LINKING" "C4 H9 N O3" 119.119 THR y THREONINE C[C@H]([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 THR 3 1 n ILE 4 1 n PHE 5 1 n VAL 6 1 n PHE 7 1 n LEU 8 1 n THR 9 1 n LEU 10 1 n ALA 11 1 n VAL 12 1 n LEU 13 1 n VAL 14 1 n SER 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 @ 2025-07-05 16:56:13)" _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 93.47 _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 88.49 1 1 A LYS 2 2 88.82 1 2 A THR 3 2 93.89 1 3 A ILE 4 2 94.64 1 4 A PHE 5 2 92.52 1 5 A VAL 6 2 96.28 1 6 A PHE 7 2 92.86 1 7 A LEU 8 2 94.42 1 8 A THR 9 2 95.64 1 9 A LEU 10 2 94.02 1 10 A ALA 11 2 97.82 1 11 A VAL 12 2 97.07 1 12 A LEU 13 2 94.12 1 13 A VAL 14 2 96.38 1 14 A SER 15 2 95.23 1 15 A SER 16 2 87.19 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 THR . 3 A 3 A 4 1 n ILE . 4 A 4 A 5 1 n PHE . 5 A 5 A 6 1 n VAL . 6 A 6 A 7 1 n PHE . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n THR . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n VAL . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n SER . 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 ? 3.689 -11.428 0.895 1.00 93.76 1 A 1 ATOM 2 C CA . MET A 1 1 ? 3.335 -10.180 1.574 1.00 94.90 1 A 1 ATOM 3 C C . MET A 1 1 ? 3.114 -9.049 0.567 1.00 94.76 1 A 1 ATOM 4 O O . MET A 1 1 ? 3.654 -7.957 0.717 1.00 93.26 1 A 1 ATOM 5 C CB . MET A 1 1 ? 4.440 -9.787 2.553 1.00 91.08 1 A 1 ATOM 6 C CG . MET A 1 1 ? 4.360 -10.513 3.873 1.00 85.40 1 A 1 ATOM 7 S SD . MET A 1 1 ? 5.700 -10.045 4.974 1.00 81.69 1 A 1 ATOM 8 C CE . MET A 1 1 ? 5.120 -10.753 6.506 1.00 73.06 1 A 1 ATOM 9 N N . LYS A 1 2 ? 2.318 -9.338 -0.447 1.00 95.74 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 2.037 -8.344 -1.474 1.00 96.07 2 A 1 ATOM 11 C C . LYS A 1 2 ? 0.662 -7.719 -1.267 1.00 96.25 2 A 1 ATOM 12 O O . LYS A 1 2 ? 0.434 -6.560 -1.606 1.00 95.22 2 A 1 ATOM 13 C CB . LYS A 1 2 ? 2.146 -8.984 -2.856 1.00 94.46 2 A 1 ATOM 14 C CG . LYS A 1 2 ? 3.508 -8.787 -3.482 1.00 87.86 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 3.796 -9.793 -4.562 1.00 84.34 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 5.216 -9.641 -5.077 1.00 78.00 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 5.672 -10.864 -5.780 1.00 71.47 2 A 1 ATOM 18 N N . THR A 1 3 ? -0.237 -8.498 -0.703 1.00 95.64 3 A 1 ATOM 19 C CA . THR A 1 3 ? -1.583 -8.012 -0.437 1.00 96.69 3 A 1 ATOM 20 C C . THR A 1 3 ? -1.552 -6.873 0.577 1.00 96.97 3 A 1 ATOM 21 O O . THR A 1 3 ? -2.309 -5.906 0.472 1.00 95.69 3 A 1 ATOM 22 C CB . THR A 1 3 ? -2.478 -9.137 0.097 1.00 95.40 3 A 1 ATOM 23 O OG1 . THR A 1 3 ? -2.091 -10.381 -0.485 1.00 89.20 3 A 1 ATOM 24 C CG2 . THR A 1 3 ? -3.930 -8.861 -0.212 1.00 87.66 3 A 1 ATOM 25 N N . ILE A 1 4 ? -0.672 -7.022 1.552 1.00 97.08 4 A 1 ATOM 26 C CA . ILE A 1 4 ? -0.526 -6.004 2.586 1.00 97.14 4 A 1 ATOM 27 C C . ILE A 1 4 ? 0.048 -4.724 1.994 1.00 97.26 4 A 1 ATOM 28 O O . ILE A 1 4 ? -0.311 -3.617 2.392 1.00 96.31 4 A 1 ATOM 29 C CB . ILE A 1 4 ? 0.383 -6.501 3.728 1.00 96.88 4 A 1 ATOM 30 C CG1 . ILE A 1 4 ? -0.058 -7.888 4.204 1.00 93.70 4 A 1 ATOM 31 C CG2 . ILE A 1 4 ? 0.372 -5.508 4.888 1.00 91.94 4 A 1 ATOM 32 C CD1 . ILE A 1 4 ? -1.475 -7.915 4.728 1.00 86.81 4 A 1 ATOM 33 N N . PHE A 1 5 ? 0.950 -4.904 1.036 1.00 95.58 5 A 1 ATOM 34 C CA . PHE A 1 5 ? 1.589 -3.777 0.369 1.00 95.97 5 A 1 ATOM 35 C C . PHE A 1 5 ? 0.554 -2.962 -0.395 1.00 96.63 5 A 1 ATOM 36 O O . PHE A 1 5 ? 0.599 -1.731 -0.409 1.00 96.31 5 A 1 ATOM 37 C CB . PHE A 1 5 ? 2.668 -4.283 -0.584 1.00 95.51 5 A 1 ATOM 38 C CG . PHE A 1 5 ? 3.942 -3.473 -0.515 1.00 92.94 5 A 1 ATOM 39 C CD1 . PHE A 1 5 ? 3.928 -2.109 -0.735 1.00 88.68 5 A 1 ATOM 40 C CD2 . PHE A 1 5 ? 5.147 -4.094 -0.232 1.00 89.72 5 A 1 ATOM 41 C CE1 . PHE A 1 5 ? 5.091 -1.365 -0.669 1.00 88.46 5 A 1 ATOM 42 C CE2 . PHE A 1 5 ? 6.321 -3.355 -0.171 1.00 89.19 5 A 1 ATOM 43 C CZ . PHE A 1 5 ? 6.291 -1.991 -0.389 1.00 88.77 5 A 1 ATOM 44 N N . VAL A 1 6 ? -0.372 -3.660 -1.012 1.00 97.53 6 A 1 ATOM 45 C CA . VAL A 1 6 ? -1.435 -3.008 -1.770 1.00 97.54 6 A 1 ATOM 46 C C . VAL A 1 6 ? -2.345 -2.214 -0.843 1.00 97.77 6 A 1 ATOM 47 O O . VAL A 1 6 ? -2.799 -1.122 -1.179 1.00 97.39 6 A 1 ATOM 48 C CB . VAL A 1 6 ? -2.261 -4.042 -2.547 1.00 96.91 6 A 1 ATOM 49 C CG1 . VAL A 1 6 ? -3.382 -3.360 -3.311 1.00 93.64 6 A 1 ATOM 50 C CG2 . VAL A 1 6 ? -1.373 -4.826 -3.497 1.00 93.16 6 A 1 ATOM 51 N N . PHE A 1 7 ? -2.607 -2.789 0.311 1.00 96.78 7 A 1 ATOM 52 C CA . PHE A 1 7 ? -3.459 -2.139 1.298 1.00 97.04 7 A 1 ATOM 53 C C . PHE A 1 7 ? -2.790 -0.879 1.830 1.00 97.37 7 A 1 ATOM 54 O O . PHE A 1 7 ? -3.442 0.145 2.039 1.00 96.92 7 A 1 ATOM 55 C CB . PHE A 1 7 ? -3.751 -3.106 2.443 1.00 96.79 7 A 1 ATOM 56 C CG . PHE A 1 7 ? -5.019 -2.775 3.189 1.00 93.05 7 A 1 ATOM 57 C CD1 . PHE A 1 7 ? -5.119 -1.621 3.940 1.00 89.03 7 A 1 ATOM 58 C CD2 . PHE A 1 7 ? -6.108 -3.630 3.136 1.00 89.57 7 A 1 ATOM 59 C CE1 . PHE A 1 7 ? -6.283 -1.304 4.621 1.00 88.42 7 A 1 ATOM 60 C CE2 . PHE A 1 7 ? -7.275 -3.320 3.820 1.00 88.16 7 A 1 ATOM 61 C CZ . PHE A 1 7 ? -7.359 -2.158 4.560 1.00 88.30 7 A 1 ATOM 62 N N . LEU A 1 8 ? -1.493 -0.980 2.034 1.00 97.41 8 A 1 ATOM 63 C CA . LEU A 1 8 ? -0.725 0.144 2.554 1.00 97.44 8 A 1 ATOM 64 C C . LEU A 1 8 ? -0.680 1.285 1.547 1.00 97.78 8 A 1 ATOM 65 O O . LEU A 1 8 ? -0.893 2.443 1.904 1.00 97.61 8 A 1 ATOM 66 C CB . LEU A 1 8 ? 0.691 -0.308 2.904 1.00 97.15 8 A 1 ATOM 67 C CG . LEU A 1 8 ? 1.549 0.740 3.617 1.00 91.22 8 A 1 ATOM 68 C CD1 . LEU A 1 8 ? 1.025 1.000 5.019 1.00 87.49 8 A 1 ATOM 69 C CD2 . LEU A 1 8 ? 3.003 0.298 3.675 1.00 89.24 8 A 1 ATOM 70 N N . THR A 1 9 ? -0.409 0.945 0.309 1.00 97.51 9 A 1 ATOM 71 C CA . THR A 1 9 ? -0.318 1.951 -0.742 1.00 97.58 9 A 1 ATOM 72 C C . THR A 1 9 ? -1.680 2.586 -1.011 1.00 97.74 9 A 1 ATOM 73 O O . THR A 1 9 ? -1.773 3.763 -1.360 1.00 97.03 9 A 1 ATOM 74 C CB . THR A 1 9 ? 0.264 1.338 -2.028 1.00 96.94 9 A 1 ATOM 75 O OG1 . THR A 1 9 ? 0.769 2.395 -2.855 1.00 92.12 9 A 1 ATOM 76 C CG2 . THR A 1 9 ? -0.765 0.553 -2.809 1.00 90.54 9 A 1 ATOM 77 N N . LEU A 1 10 ? -2.724 1.795 -0.836 1.00 98.02 10 A 1 ATOM 78 C CA . LEU A 1 10 ? -4.084 2.285 -1.031 1.00 97.82 10 A 1 ATOM 79 C C . LEU A 1 10 ? -4.452 3.285 0.057 1.00 97.99 10 A 1 ATOM 80 O O . LEU A 1 10 ? -5.140 4.274 -0.202 1.00 97.59 10 A 1 ATOM 81 C CB . LEU A 1 10 ? -5.066 1.113 -1.016 1.00 97.18 10 A 1 ATOM 82 C CG . LEU A 1 10 ? -6.469 1.457 -1.499 1.00 89.72 10 A 1 ATOM 83 C CD1 . LEU A 1 10 ? -6.479 1.703 -2.995 1.00 85.97 10 A 1 ATOM 84 C CD2 . LEU A 1 10 ? -7.444 0.349 -1.140 1.00 87.90 10 A 1 ATOM 85 N N . ALA A 1 11 ? -4.004 2.998 1.266 1.00 98.03 11 A 1 ATOM 86 C CA . ALA A 1 11 ? -4.268 3.873 2.401 1.00 98.04 11 A 1 ATOM 87 C C . ALA A 1 11 ? -3.589 5.224 2.213 1.00 98.18 11 A 1 ATOM 88 O O . ALA A 1 11 ? -4.142 6.261 2.570 1.00 97.36 11 A 1 ATOM 89 C CB . ALA A 1 11 ? -3.790 3.219 3.692 1.00 97.49 11 A 1 ATOM 90 N N . VAL A 1 12 ? -2.396 5.189 1.656 1.00 98.20 12 A 1 ATOM 91 C CA . VAL A 1 12 ? -1.637 6.413 1.411 1.00 98.11 12 A 1 ATOM 92 C C . VAL A 1 12 ? -2.294 7.236 0.312 1.00 98.23 12 A 1 ATOM 93 O O . VAL A 1 12 ? -2.319 8.469 0.376 1.00 97.63 12 A 1 ATOM 94 C CB . VAL A 1 12 ? -0.182 6.093 1.027 1.00 97.57 12 A 1 ATOM 95 C CG1 . VAL A 1 12 ? 0.594 7.372 0.741 1.00 94.91 12 A 1 ATOM 96 C CG2 . VAL A 1 12 ? 0.499 5.304 2.130 1.00 94.81 12 A 1 ATOM 97 N N . LEU A 1 13 ? -2.830 6.554 -0.671 1.00 98.01 13 A 1 ATOM 98 C CA . LEU A 1 13 ? -3.485 7.215 -1.794 1.00 97.84 13 A 1 ATOM 99 C C . LEU A 1 13 ? -4.787 7.875 -1.364 1.00 97.99 13 A 1 ATOM 100 O O . LEU A 1 13 ? -5.097 8.989 -1.790 1.00 97.30 13 A 1 ATOM 101 C CB . LEU A 1 13 ? -3.755 6.203 -2.906 1.00 97.21 13 A 1 ATOM 102 C CG . LEU A 1 13 ? -4.126 6.824 -4.248 1.00 91.13 13 A 1 ATOM 103 C CD1 . LEU A 1 13 ? -2.919 7.491 -4.884 1.00 86.34 13 A 1 ATOM 104 C CD2 . LEU A 1 13 ? -4.706 5.776 -5.177 1.00 87.18 13 A 1 ATOM 105 N N . VAL A 1 14 ? -5.541 7.174 -0.541 1.00 98.29 14 A 1 ATOM 106 C CA . VAL A 1 14 ? -6.817 7.699 -0.058 1.00 98.11 14 A 1 ATOM 107 C C . VAL A 1 14 ? -6.603 8.837 0.936 1.00 98.10 14 A 1 ATOM 108 O O . VAL A 1 14 ? -7.440 9.736 1.062 1.00 97.20 14 A 1 ATOM 109 C CB . VAL A 1 14 ? -7.663 6.579 0.589 1.00 97.24 14 A 1 ATOM 110 C CG1 . VAL A 1 14 ? -7.084 6.171 1.937 1.00 92.42 14 A 1 ATOM 111 C CG2 . VAL A 1 14 ? -9.104 7.018 0.748 1.00 93.29 14 A 1 ATOM 112 N N . SER A 1 15 ? -5.484 8.772 1.639 1.00 97.63 15 A 1 ATOM 113 C CA . SER A 1 15 ? -5.146 9.799 2.620 1.00 97.42 15 A 1 ATOM 114 C C . SER A 1 15 ? -4.601 11.047 1.937 1.00 97.04 15 A 1 ATOM 115 O O . SER A 1 15 ? -4.823 12.174 2.388 1.00 94.66 15 A 1 ATOM 116 C CB . SER A 1 15 ? -4.128 9.264 3.625 1.00 96.16 15 A 1 ATOM 117 O OG . SER A 1 15 ? -4.031 10.113 4.744 1.00 88.50 15 A 1 ATOM 118 N N . SER A 1 16 ? -3.883 10.809 0.859 1.00 95.08 16 A 1 ATOM 119 C CA . SER A 1 16 ? -3.277 11.899 0.109 1.00 92.76 16 A 1 ATOM 120 C C . SER A 1 16 ? -3.998 12.143 -1.218 1.00 89.50 16 A 1 ATOM 121 O O . SER A 1 16 ? -4.756 11.265 -1.671 1.00 83.67 16 A 1 ATOM 122 C CB . SER A 1 16 ? -1.796 11.624 -0.147 1.00 88.53 16 A 1 ATOM 123 O OG . SER A 1 16 ? -1.137 12.793 -0.589 1.00 79.88 16 A 1 ATOM 124 O OXT . SER A 1 16 ? -3.800 13.175 -1.837 1.00 80.93 16 A 1 #