# 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_spkb07939 # _entry.id spkb07939 # 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 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" "C5 H9 N O2" 115.130 PRO y PROLINE C1C[C@H](NC1)C(=O)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" "C9 H11 N O3" 181.189 TYR y TYROSINE c1cc(ccc1C[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 HIS 2 1 n TYR 3 1 n LEU 4 1 n ALA 5 1 n VAL 6 1 n ALA 7 1 n LEU 8 1 n PRO 9 1 n LEU 10 1 n LEU 11 1 n THR 12 1 n LEU 13 1 n ALA 14 1 n LEU 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 @ 2025-07-03 17:10:21)" _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 93.56 _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 85.09 1 1 A HIS 2 2 85.25 1 2 A TYR 3 2 91.23 1 3 A LEU 4 2 93.54 1 4 A ALA 5 2 96.73 1 5 A VAL 6 2 96.29 1 6 A ALA 7 2 97.77 1 7 A LEU 8 2 95.63 1 8 A PRO 9 2 97.52 1 9 A LEU 10 2 96.60 1 10 A LEU 11 2 95.39 1 11 A THR 12 2 95.39 1 12 A LEU 13 2 95.97 1 13 A ALA 14 2 97.97 1 14 A LEU 15 2 94.54 1 15 A ALA 16 2 89.77 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 HIS . 2 A 2 A 3 1 n TYR . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n VAL . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n PRO . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n THR . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n LEU . 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 ? -2.611 12.497 1.026 1.00 90.04 1 A 1 ATOM 2 C CA . MET A 1 1 ? -3.538 11.376 0.843 1.00 90.70 1 A 1 ATOM 3 C C . MET A 1 1 ? -3.053 10.429 -0.263 1.00 91.05 1 A 1 ATOM 4 O O . MET A 1 1 ? -3.482 10.529 -1.405 1.00 89.39 1 A 1 ATOM 5 C CB . MET A 1 1 ? -4.936 11.902 0.511 1.00 87.28 1 A 1 ATOM 6 C CG . MET A 1 1 ? -4.943 12.951 -0.596 1.00 83.05 1 A 1 ATOM 7 S SD . MET A 1 1 ? -6.532 13.786 -0.720 1.00 79.36 1 A 1 ATOM 8 C CE . MET A 1 1 ? -6.005 15.480 -0.645 1.00 69.89 1 A 1 ATOM 9 N N . HIS A 1 2 ? -2.169 9.512 0.081 1.00 90.43 2 A 1 ATOM 10 C CA . HIS A 1 2 ? -1.642 8.549 -0.876 1.00 91.73 2 A 1 ATOM 11 C C . HIS A 1 2 ? -1.473 7.170 -0.235 1.00 93.82 2 A 1 ATOM 12 O O . HIS A 1 2 ? -0.592 6.398 -0.605 1.00 92.64 2 A 1 ATOM 13 C CB . HIS A 1 2 ? -0.309 9.050 -1.440 1.00 89.59 2 A 1 ATOM 14 C CG . HIS A 1 2 ? -0.384 9.388 -2.899 1.00 85.80 2 A 1 ATOM 15 N ND1 . HIS A 1 2 ? 0.095 10.566 -3.423 1.00 78.10 2 A 1 ATOM 16 C CD2 . HIS A 1 2 ? -0.881 8.684 -3.944 1.00 74.82 2 A 1 ATOM 17 C CE1 . HIS A 1 2 ? -0.107 10.568 -4.733 1.00 78.10 2 A 1 ATOM 18 N NE2 . HIS A 1 2 ? -0.698 9.431 -5.080 1.00 77.45 2 A 1 ATOM 19 N N . TYR A 1 3 ? -2.315 6.866 0.734 1.00 93.81 3 A 1 ATOM 20 C CA . TYR A 1 3 ? -2.248 5.588 1.439 1.00 95.31 3 A 1 ATOM 21 C C . TYR A 1 3 ? -2.742 4.435 0.569 1.00 96.40 3 A 1 ATOM 22 O O . TYR A 1 3 ? -2.204 3.330 0.630 1.00 95.77 3 A 1 ATOM 23 C CB . TYR A 1 3 ? -3.087 5.655 2.713 1.00 94.37 3 A 1 ATOM 24 C CG . TYR A 1 3 ? -2.591 6.708 3.678 1.00 91.22 3 A 1 ATOM 25 C CD1 . TYR A 1 3 ? -1.362 6.564 4.309 1.00 89.32 3 A 1 ATOM 26 C CD2 . TYR A 1 3 ? -3.360 7.826 3.962 1.00 88.32 3 A 1 ATOM 27 C CE1 . TYR A 1 3 ? -0.903 7.525 5.197 1.00 88.49 3 A 1 ATOM 28 C CE2 . TYR A 1 3 ? -2.908 8.795 4.851 1.00 87.72 3 A 1 ATOM 29 C CZ . TYR A 1 3 ? -1.679 8.634 5.464 1.00 88.03 3 A 1 ATOM 30 O OH . TYR A 1 3 ? -1.233 9.586 6.341 1.00 86.05 3 A 1 ATOM 31 N N . LEU A 1 4 ? -3.755 4.687 -0.255 1.00 95.28 4 A 1 ATOM 32 C CA . LEU A 1 4 ? -4.326 3.663 -1.129 1.00 95.63 4 A 1 ATOM 33 C C . LEU A 1 4 ? -3.294 3.116 -2.109 1.00 96.45 4 A 1 ATOM 34 O O . LEU A 1 4 ? -3.198 1.905 -2.306 1.00 96.21 4 A 1 ATOM 35 C CB . LEU A 1 4 ? -5.515 4.247 -1.904 1.00 95.20 4 A 1 ATOM 36 C CG . LEU A 1 4 ? -6.759 4.499 -1.060 1.00 91.95 4 A 1 ATOM 37 C CD1 . LEU A 1 4 ? -7.666 5.508 -1.738 1.00 89.17 4 A 1 ATOM 38 C CD2 . LEU A 1 4 ? -7.503 3.191 -0.830 1.00 88.43 4 A 1 ATOM 39 N N . ALA A 1 5 ? -2.531 4.001 -2.716 1.00 96.67 5 A 1 ATOM 40 C CA . ALA A 1 5 ? -1.521 3.610 -3.694 1.00 96.83 5 A 1 ATOM 41 C C . ALA A 1 5 ? -0.318 2.934 -3.038 1.00 97.30 5 A 1 ATOM 42 O O . ALA A 1 5 ? 0.373 2.143 -3.673 1.00 96.89 5 A 1 ATOM 43 C CB . ALA A 1 5 ? -1.077 4.834 -4.486 1.00 95.96 5 A 1 ATOM 44 N N . VAL A 1 6 ? -0.071 3.222 -1.781 1.00 97.18 6 A 1 ATOM 45 C CA . VAL A 1 6 ? 1.061 2.656 -1.045 1.00 97.18 6 A 1 ATOM 46 C C . VAL A 1 6 ? 0.657 1.421 -0.240 1.00 97.65 6 A 1 ATOM 47 O O . VAL A 1 6 ? 1.424 0.464 -0.133 1.00 97.50 6 A 1 ATOM 48 C CB . VAL A 1 6 ? 1.682 3.714 -0.115 1.00 96.49 6 A 1 ATOM 49 C CG1 . VAL A 1 6 ? 2.879 3.149 0.625 1.00 94.09 6 A 1 ATOM 50 C CG2 . VAL A 1 6 ? 2.090 4.945 -0.906 1.00 93.97 6 A 1 ATOM 51 N N . ALA A 1 7 ? -0.535 1.447 0.312 1.00 97.73 7 A 1 ATOM 52 C CA . ALA A 1 7 ? -1.022 0.350 1.141 1.00 97.83 7 A 1 ATOM 53 C C . ALA A 1 7 ? -1.324 -0.907 0.328 1.00 98.06 7 A 1 ATOM 54 O O . ALA A 1 7 ? -1.057 -2.021 0.782 1.00 97.70 7 A 1 ATOM 55 C CB . ALA A 1 7 ? -2.268 0.791 1.900 1.00 97.51 7 A 1 ATOM 56 N N . LEU A 1 8 ? -1.879 -0.735 -0.844 1.00 97.60 8 A 1 ATOM 57 C CA . LEU A 1 8 ? -2.232 -1.857 -1.715 1.00 97.50 8 A 1 ATOM 58 C C . LEU A 1 8 ? -1.012 -2.708 -2.079 1.00 97.73 8 A 1 ATOM 59 O O . LEU A 1 8 ? -1.010 -3.916 -1.830 1.00 97.48 8 A 1 ATOM 60 C CB . LEU A 1 8 ? -2.930 -1.337 -2.974 1.00 97.06 8 A 1 ATOM 61 C CG . LEU A 1 8 ? -3.744 -2.389 -3.711 1.00 93.90 8 A 1 ATOM 62 C CD1 . LEU A 1 8 ? -5.167 -1.900 -3.943 1.00 92.21 8 A 1 ATOM 63 C CD2 . LEU A 1 8 ? -3.092 -2.738 -5.035 1.00 91.60 8 A 1 ATOM 64 N N . PRO A 1 9 ? 0.023 -2.115 -2.671 1.00 97.80 9 A 1 ATOM 65 C CA . PRO A 1 9 ? 1.221 -2.878 -3.047 1.00 97.77 9 A 1 ATOM 66 C C . PRO A 1 9 ? 1.962 -3.431 -1.839 1.00 98.09 9 A 1 ATOM 67 O O . PRO A 1 9 ? 2.560 -4.504 -1.915 1.00 97.77 9 A 1 ATOM 68 C CB . PRO A 1 9 ? 2.083 -1.855 -3.798 1.00 97.25 9 A 1 ATOM 69 C CG . PRO A 1 9 ? 1.598 -0.532 -3.352 1.00 96.51 9 A 1 ATOM 70 C CD . PRO A 1 9 ? 0.135 -0.702 -3.072 1.00 97.46 9 A 1 ATOM 71 N N . LEU A 1 10 ? 1.918 -2.733 -0.736 1.00 97.42 10 A 1 ATOM 72 C CA . LEU A 1 10 ? 2.577 -3.168 0.489 1.00 97.50 10 A 1 ATOM 73 C C . LEU A 1 10 ? 1.906 -4.416 1.044 1.00 97.75 10 A 1 ATOM 74 O O . LEU A 1 10 ? 2.576 -5.344 1.504 1.00 97.34 10 A 1 ATOM 75 C CB . LEU A 1 10 ? 2.536 -2.038 1.523 1.00 97.19 10 A 1 ATOM 76 C CG . LEU A 1 10 ? 3.914 -1.547 1.956 1.00 95.95 10 A 1 ATOM 77 C CD1 . LEU A 1 10 ? 3.831 -0.155 2.558 1.00 95.04 10 A 1 ATOM 78 C CD2 . LEU A 1 10 ? 4.530 -2.518 2.952 1.00 94.61 10 A 1 ATOM 79 N N . LEU A 1 11 ? 0.588 -4.441 0.991 1.00 97.38 11 A 1 ATOM 80 C CA . LEU A 1 11 ? -0.189 -5.577 1.474 1.00 97.09 11 A 1 ATOM 81 C C . LEU A 1 11 ? 0.055 -6.800 0.605 1.00 97.47 11 A 1 ATOM 82 O O . LEU A 1 11 ? 0.174 -7.919 1.108 1.00 96.98 11 A 1 ATOM 83 C CB . LEU A 1 11 ? -1.676 -5.217 1.484 1.00 96.68 11 A 1 ATOM 84 C CG . LEU A 1 11 ? -2.483 -5.961 2.537 1.00 93.60 11 A 1 ATOM 85 C CD1 . LEU A 1 11 ? -3.399 -5.003 3.284 1.00 91.99 11 A 1 ATOM 86 C CD2 . LEU A 1 11 ? -3.295 -7.072 1.905 1.00 91.94 11 A 1 ATOM 87 N N . THR A 1 12 ? 0.125 -6.589 -0.690 1.00 96.66 12 A 1 ATOM 88 C CA . THR A 1 12 ? 0.367 -7.669 -1.644 1.00 96.47 12 A 1 ATOM 89 C C . THR A 1 12 ? 1.745 -8.283 -1.423 1.00 97.14 12 A 1 ATOM 90 O O . THR A 1 12 ? 1.920 -9.499 -1.533 1.00 96.73 12 A 1 ATOM 91 C CB . THR A 1 12 ? 0.260 -7.139 -3.078 1.00 95.75 12 A 1 ATOM 92 O OG1 . THR A 1 12 ? -0.989 -6.480 -3.250 1.00 93.10 12 A 1 ATOM 93 C CG2 . THR A 1 12 ? 0.346 -8.274 -4.086 1.00 91.87 12 A 1 ATOM 94 N N . LEU A 1 13 ? 2.707 -7.468 -1.102 1.00 97.61 13 A 1 ATOM 95 C CA . LEU A 1 13 ? 4.070 -7.917 -0.855 1.00 97.53 13 A 1 ATOM 96 C C . LEU A 1 13 ? 4.129 -8.805 0.383 1.00 97.92 13 A 1 ATOM 97 O O . LEU A 1 13 ? 4.854 -9.799 0.408 1.00 97.53 13 A 1 ATOM 98 C CB . LEU A 1 13 ? 4.987 -6.705 -0.671 1.00 97.03 13 A 1 ATOM 99 C CG . LEU A 1 13 ? 6.471 -7.038 -0.669 1.00 94.62 13 A 1 ATOM 100 C CD1 . LEU A 1 13 ? 6.953 -7.318 -2.083 1.00 93.04 13 A 1 ATOM 101 C CD2 . LEU A 1 13 ? 7.267 -5.911 -0.055 1.00 92.49 13 A 1 ATOM 102 N N . ALA A 1 14 ? 3.369 -8.454 1.390 1.00 97.99 14 A 1 ATOM 103 C CA . ALA A 1 14 ? 3.323 -9.220 2.631 1.00 98.01 14 A 1 ATOM 104 C C . ALA A 1 14 ? 2.584 -10.541 2.445 1.00 98.25 14 A 1 ATOM 105 O O . ALA A 1 14 ? 2.888 -11.528 3.123 1.00 97.87 14 A 1 ATOM 106 C CB . ALA A 1 14 ? 2.654 -8.394 3.725 1.00 97.71 14 A 1 ATOM 107 N N . LEU A 1 15 ? 1.624 -10.564 1.535 1.00 96.95 15 A 1 ATOM 108 C CA . LEU A 1 15 ? 0.833 -11.755 1.263 1.00 96.69 15 A 1 ATOM 109 C C . LEU A 1 15 ? 1.598 -12.746 0.395 1.00 96.92 15 A 1 ATOM 110 O O . LEU A 1 15 ? 1.666 -13.939 0.707 1.00 95.98 15 A 1 ATOM 111 C CB . LEU A 1 15 ? -0.479 -11.359 0.582 1.00 95.79 15 A 1 ATOM 112 C CG . LEU A 1 15 ? -1.581 -10.896 1.535 1.00 93.53 15 A 1 ATOM 113 C CD1 . LEU A 1 15 ? -2.664 -10.153 0.785 1.00 91.20 15 A 1 ATOM 114 C CD2 . LEU A 1 15 ? -2.169 -12.096 2.266 1.00 89.29 15 A 1 ATOM 115 N N . ALA A 1 16 ? 2.150 -12.258 -0.681 1.00 94.99 16 A 1 ATOM 116 C CA . ALA A 1 16 ? 2.897 -13.086 -1.630 1.00 93.04 16 A 1 ATOM 117 C C . ALA A 1 16 ? 4.387 -12.846 -1.483 1.00 91.39 16 A 1 ATOM 118 O O . ALA A 1 16 ? 5.152 -13.832 -1.438 1.00 89.01 16 A 1 ATOM 119 C CB . ALA A 1 16 ? 2.438 -12.782 -3.051 1.00 89.13 16 A 1 ATOM 120 O OXT . ALA A 1 16 ? 4.779 -11.683 -1.434 1.00 81.03 16 A 1 #