# 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_spkb40769 # _entry.id spkb40769 # 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 PHE 3 1 n ILE 4 1 n ILE 5 1 n ILE 6 1 n LEU 7 1 n PHE 8 1 n THR 9 1 n LEU 10 1 n ILE 11 1 n SER 12 1 n ILE 13 1 n VAL 14 1 n THR 15 1 n ALA 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 @ 2025-07-10 19:07:20)" _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 95.41 _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 89.46 1 1 A LYS 2 2 91.28 1 2 A PHE 3 2 94.10 1 3 A ILE 4 2 96.96 1 4 A ILE 5 2 97.57 1 5 A ILE 6 2 97.55 1 6 A LEU 7 2 96.53 1 7 A PHE 8 2 93.84 1 8 A THR 9 2 96.91 1 9 A LEU 10 2 95.81 1 10 A ILE 11 2 97.17 1 11 A SER 12 2 97.33 1 12 A ILE 13 2 97.56 1 13 A VAL 14 2 97.27 1 14 A THR 15 2 96.29 1 15 A ALA 16 2 92.86 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 PHE . 3 A 3 A 4 1 n ILE . 4 A 4 A 5 1 n ILE . 5 A 5 A 6 1 n ILE . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n PHE . 8 A 8 A 9 1 n THR . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n ILE . 11 A 11 A 12 1 n SER . 12 A 12 A 13 1 n ILE . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n THR . 15 A 15 A 16 1 n ALA . 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 ? -7.826 11.925 3.956 1.00 94.23 1 A 1 ATOM 2 C CA . MET A 1 1 ? -6.972 10.817 4.416 1.00 95.64 1 A 1 ATOM 3 C C . MET A 1 1 ? -5.920 10.474 3.368 1.00 95.89 1 A 1 ATOM 4 O O . MET A 1 1 ? -6.218 9.828 2.370 1.00 93.99 1 A 1 ATOM 5 C CB . MET A 1 1 ? -7.822 9.584 4.702 1.00 92.79 1 A 1 ATOM 6 C CG . MET A 1 1 ? -8.601 9.724 5.991 1.00 85.70 1 A 1 ATOM 7 S SD . MET A 1 1 ? -9.330 8.179 6.510 1.00 83.18 1 A 1 ATOM 8 C CE . MET A 1 1 ? -9.668 8.549 8.222 1.00 74.23 1 A 1 ATOM 9 N N . LYS A 1 2 ? -4.702 10.925 3.592 1.00 97.55 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -3.608 10.677 2.659 1.00 97.55 2 A 1 ATOM 11 C C . LYS A 1 2 ? -2.663 9.599 3.175 1.00 97.84 2 A 1 ATOM 12 O O . LYS A 1 2 ? -1.888 9.034 2.411 1.00 97.38 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -2.840 11.969 2.427 1.00 96.67 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -3.673 13.033 1.750 1.00 91.38 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -3.168 14.423 2.085 1.00 87.47 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -4.075 15.478 1.483 1.00 80.94 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -4.224 16.624 2.384 1.00 74.77 2 A 1 ATOM 18 N N . PHE A 1 3 ? -2.727 9.328 4.458 1.00 97.65 3 A 1 ATOM 19 C CA . PHE A 1 3 ? -1.864 8.322 5.065 1.00 98.02 3 A 1 ATOM 20 C C . PHE A 1 3 ? -2.295 6.914 4.685 1.00 98.33 3 A 1 ATOM 21 O O . PHE A 1 3 ? -1.484 5.991 4.680 1.00 97.97 3 A 1 ATOM 22 C CB . PHE A 1 3 ? -1.876 8.469 6.585 1.00 97.49 3 A 1 ATOM 23 C CG . PHE A 1 3 ? -0.640 9.149 7.115 1.00 94.41 3 A 1 ATOM 24 C CD1 . PHE A 1 3 ? 0.567 8.479 7.130 1.00 90.99 3 A 1 ATOM 25 C CD2 . PHE A 1 3 ? -0.701 10.440 7.593 1.00 90.99 3 A 1 ATOM 26 C CE1 . PHE A 1 3 ? 1.711 9.088 7.613 1.00 89.97 3 A 1 ATOM 27 C CE2 . PHE A 1 3 ? 0.439 11.061 8.080 1.00 90.38 3 A 1 ATOM 28 C CZ . PHE A 1 3 ? 1.646 10.384 8.092 1.00 88.92 3 A 1 ATOM 29 N N . ILE A 1 4 ? -3.571 6.772 4.365 1.00 98.12 4 A 1 ATOM 30 C CA . ILE A 1 4 ? -4.102 5.469 3.982 1.00 98.26 4 A 1 ATOM 31 C C . ILE A 1 4 ? -3.413 4.964 2.725 1.00 98.38 4 A 1 ATOM 32 O O . ILE A 1 4 ? -3.084 3.788 2.605 1.00 98.07 4 A 1 ATOM 33 C CB . ILE A 1 4 ? -5.620 5.543 3.753 1.00 98.05 4 A 1 ATOM 34 C CG1 . ILE A 1 4 ? -6.312 6.199 4.955 1.00 96.57 4 A 1 ATOM 35 C CG2 . ILE A 1 4 ? -6.185 4.148 3.504 1.00 95.91 4 A 1 ATOM 36 C CD1 . ILE A 1 4 ? -6.081 5.462 6.260 1.00 92.35 4 A 1 ATOM 37 N N . ILE A 1 5 ? -3.210 5.857 1.784 1.00 98.40 5 A 1 ATOM 38 C CA . ILE A 1 5 ? -2.563 5.514 0.525 1.00 98.36 5 A 1 ATOM 39 C C . ILE A 1 5 ? -1.088 5.219 0.741 1.00 98.35 5 A 1 ATOM 40 O O . ILE A 1 5 ? -0.533 4.285 0.167 1.00 98.18 5 A 1 ATOM 41 C CB . ILE A 1 5 ? -2.720 6.652 -0.492 1.00 98.25 5 A 1 ATOM 42 C CG1 . ILE A 1 5 ? -4.190 7.083 -0.594 1.00 97.36 5 A 1 ATOM 43 C CG2 . ILE A 1 5 ? -2.184 6.219 -1.849 1.00 97.16 5 A 1 ATOM 44 C CD1 . ILE A 1 5 ? -5.113 5.959 -1.014 1.00 94.52 5 A 1 ATOM 45 N N . ILE A 1 6 ? -0.458 6.033 1.545 1.00 98.50 6 A 1 ATOM 46 C CA . ILE A 1 6 ? 0.964 5.871 1.836 1.00 98.42 6 A 1 ATOM 47 C C . ILE A 1 6 ? 1.209 4.594 2.625 1.00 98.39 6 A 1 ATOM 48 O O . ILE A 1 6 ? 2.204 3.900 2.414 1.00 98.26 6 A 1 ATOM 49 C CB . ILE A 1 6 ? 1.495 7.076 2.630 1.00 98.40 6 A 1 ATOM 50 C CG1 . ILE A 1 6 ? 1.286 8.369 1.845 1.00 97.43 6 A 1 ATOM 51 C CG2 . ILE A 1 6 ? 2.976 6.888 2.945 1.00 97.07 6 A 1 ATOM 52 C CD1 . ILE A 1 6 ? 1.422 9.599 2.712 1.00 93.92 6 A 1 ATOM 53 N N . LEU A 1 7 ? 0.303 4.302 3.523 1.00 98.24 7 A 1 ATOM 54 C CA . LEU A 1 7 ? 0.423 3.107 4.349 1.00 98.20 7 A 1 ATOM 55 C C . LEU A 1 7 ? 0.296 1.851 3.501 1.00 98.26 7 A 1 ATOM 56 O O . LEU A 1 7 ? 1.043 0.891 3.677 1.00 98.23 7 A 1 ATOM 57 C CB . LEU A 1 7 ? -0.655 3.117 5.434 1.00 98.12 7 A 1 ATOM 58 C CG . LEU A 1 7 ? -0.416 2.119 6.565 1.00 95.04 7 A 1 ATOM 59 C CD1 . LEU A 1 7 ? 0.627 2.663 7.536 1.00 92.58 7 A 1 ATOM 60 C CD2 . LEU A 1 7 ? -1.710 1.830 7.313 1.00 93.58 7 A 1 ATOM 61 N N . PHE A 1 8 ? -0.653 1.864 2.586 1.00 97.92 8 A 1 ATOM 62 C CA . PHE A 1 8 ? -0.893 0.722 1.712 1.00 97.81 8 A 1 ATOM 63 C C . PHE A 1 8 ? 0.226 0.565 0.695 1.00 98.03 8 A 1 ATOM 64 O O . PHE A 1 8 ? 0.676 -0.549 0.429 1.00 97.72 8 A 1 ATOM 65 C CB . PHE A 1 8 ? -2.226 0.891 0.996 1.00 97.45 8 A 1 ATOM 66 C CG . PHE A 1 8 ? -2.667 -0.364 0.294 1.00 93.63 8 A 1 ATOM 67 C CD1 . PHE A 1 8 ? -2.319 -0.589 -1.028 1.00 89.99 8 A 1 ATOM 68 C CD2 . PHE A 1 8 ? -3.415 -1.314 0.967 1.00 91.08 8 A 1 ATOM 69 C CE1 . PHE A 1 8 ? -2.713 -1.748 -1.673 1.00 89.53 8 A 1 ATOM 70 C CE2 . PHE A 1 8 ? -3.811 -2.477 0.323 1.00 89.73 8 A 1 ATOM 71 C CZ . PHE A 1 8 ? -3.459 -2.692 -0.995 1.00 89.34 8 A 1 ATOM 72 N N . THR A 1 9 ? 0.662 1.665 0.142 1.00 97.89 9 A 1 ATOM 73 C CA . THR A 1 9 ? 1.715 1.635 -0.867 1.00 98.03 9 A 1 ATOM 74 C C . THR A 1 9 ? 3.029 1.145 -0.272 1.00 98.25 9 A 1 ATOM 75 O O . THR A 1 9 ? 3.810 0.479 -0.946 1.00 97.88 9 A 1 ATOM 76 C CB . THR A 1 9 ? 1.903 3.022 -1.498 1.00 97.65 9 A 1 ATOM 77 O OG1 . THR A 1 9 ? 2.738 2.901 -2.645 1.00 94.94 9 A 1 ATOM 78 C CG2 . THR A 1 9 ? 2.530 4.004 -0.538 1.00 93.73 9 A 1 ATOM 79 N N . LEU A 1 10 ? 3.258 1.461 0.979 1.00 98.32 10 A 1 ATOM 80 C CA . LEU A 1 10 ? 4.476 1.040 1.663 1.00 98.29 10 A 1 ATOM 81 C C . LEU A 1 10 ? 4.529 -0.474 1.769 1.00 98.39 10 A 1 ATOM 82 O O . LEU A 1 10 ? 5.551 -1.094 1.486 1.00 98.17 10 A 1 ATOM 83 C CB . LEU A 1 10 ? 4.524 1.657 3.058 1.00 98.06 10 A 1 ATOM 84 C CG . LEU A 1 10 ? 5.926 1.713 3.649 1.00 92.75 10 A 1 ATOM 85 C CD1 . LEU A 1 10 ? 6.612 3.003 3.239 1.00 90.20 10 A 1 ATOM 86 C CD2 . LEU A 1 10 ? 5.871 1.612 5.167 1.00 92.32 10 A 1 ATOM 87 N N . ILE A 1 11 ? 3.430 -1.056 2.172 1.00 98.49 11 A 1 ATOM 88 C CA . ILE A 1 11 ? 3.338 -2.507 2.309 1.00 98.39 11 A 1 ATOM 89 C C . ILE A 1 11 ? 3.343 -3.170 0.943 1.00 98.42 11 A 1 ATOM 90 O O . ILE A 1 11 ? 3.873 -4.267 0.776 1.00 98.07 11 A 1 ATOM 91 C CB . ILE A 1 11 ? 2.065 -2.889 3.078 1.00 98.08 11 A 1 ATOM 92 C CG1 . ILE A 1 11 ? 2.095 -2.279 4.478 1.00 96.68 11 A 1 ATOM 93 C CG2 . ILE A 1 11 ? 1.935 -4.407 3.172 1.00 96.31 11 A 1 ATOM 94 C CD1 . ILE A 1 11 ? 0.724 -2.154 5.097 1.00 92.91 11 A 1 ATOM 95 N N . SER A 1 12 ? 2.768 -2.508 -0.017 1.00 98.53 12 A 1 ATOM 96 C CA . SER A 1 12 ? 2.693 -3.026 -1.378 1.00 98.48 12 A 1 ATOM 97 C C . SER A 1 12 ? 4.082 -3.183 -1.982 1.00 98.58 12 A 1 ATOM 98 O O . SER A 1 12 ? 4.358 -4.151 -2.682 1.00 98.19 12 A 1 ATOM 99 C CB . SER A 1 12 ? 1.860 -2.096 -2.241 1.00 98.02 12 A 1 ATOM 100 O OG . SER A 1 12 ? 1.638 -2.670 -3.495 1.00 92.21 12 A 1 ATOM 101 N N . ILE A 1 13 ? 4.956 -2.248 -1.701 1.00 98.57 13 A 1 ATOM 102 C CA . ILE A 1 13 ? 6.324 -2.282 -2.208 1.00 98.52 13 A 1 ATOM 103 C C . ILE A 1 13 ? 7.109 -3.415 -1.570 1.00 98.57 13 A 1 ATOM 104 O O . ILE A 1 13 ? 7.892 -4.091 -2.234 1.00 98.15 13 A 1 ATOM 105 C CB . ILE A 1 13 ? 7.030 -0.945 -1.941 1.00 98.24 13 A 1 ATOM 106 C CG1 . ILE A 1 13 ? 6.363 0.168 -2.742 1.00 96.98 13 A 1 ATOM 107 C CG2 . ILE A 1 13 ? 8.505 -1.039 -2.317 1.00 96.45 13 A 1 ATOM 108 C CD1 . ILE A 1 13 ? 6.665 1.542 -2.202 1.00 94.97 13 A 1 ATOM 109 N N . VAL A 1 14 ? 6.907 -3.611 -0.289 1.00 98.43 14 A 1 ATOM 110 C CA . VAL A 1 14 ? 7.597 -4.670 0.441 1.00 98.34 14 A 1 ATOM 111 C C . VAL A 1 14 ? 7.135 -6.033 -0.034 1.00 98.41 14 A 1 ATOM 112 O O . VAL A 1 14 ? 7.945 -6.940 -0.230 1.00 97.71 14 A 1 ATOM 113 C CB . VAL A 1 14 ? 7.358 -4.540 1.951 1.00 97.77 14 A 1 ATOM 114 C CG1 . VAL A 1 14 ? 8.071 -5.655 2.695 1.00 95.23 14 A 1 ATOM 115 C CG2 . VAL A 1 14 ? 7.840 -3.196 2.451 1.00 95.02 14 A 1 ATOM 116 N N . THR A 1 15 ? 5.845 -6.176 -0.209 1.00 98.12 15 A 1 ATOM 117 C CA . THR A 1 15 ? 5.268 -7.435 -0.662 1.00 98.09 15 A 1 ATOM 118 C C . THR A 1 15 ? 5.482 -7.624 -2.154 1.00 98.04 15 A 1 ATOM 119 O O . THR A 1 15 ? 5.744 -8.735 -2.612 1.00 96.90 15 A 1 ATOM 120 C CB . THR A 1 15 ? 3.772 -7.484 -0.348 1.00 97.17 15 A 1 ATOM 121 O OG1 . THR A 1 15 ? 3.566 -7.146 1.019 1.00 93.13 15 A 1 ATOM 122 C CG2 . THR A 1 15 ? 3.222 -8.876 -0.603 1.00 92.60 15 A 1 ATOM 123 N N . ALA A 1 16 ? 5.381 -6.515 -2.893 1.00 96.75 16 A 1 ATOM 124 C CA . ALA A 1 16 ? 5.557 -6.510 -4.347 1.00 95.82 16 A 1 ATOM 125 C C . ALA A 1 16 ? 4.638 -7.522 -5.022 1.00 94.97 16 A 1 ATOM 126 O O . ALA A 1 16 ? 5.022 -8.685 -5.189 1.00 91.56 16 A 1 ATOM 127 C CB . ALA A 1 16 ? 7.003 -6.794 -4.707 1.00 93.82 16 A 1 ATOM 128 O OXT . ALA A 1 16 ? 3.519 -7.114 -5.398 1.00 84.26 16 A 1 #