# 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_spkb12785 # _entry.id spkb12785 # 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" "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" "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" # _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 PRO 2 1 n PRO 3 1 n THR 4 1 n LEU 5 1 n LEU 6 1 n LEU 7 1 n LEU 8 1 n LEU 9 1 n LEU 10 1 n LEU 11 1 n LEU 12 1 n PRO 13 1 n PRO 14 1 n SER 15 1 n LEU 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 @ 2025-07-09 06:54:56)" _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 87.27 _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 77.52 1 1 A PRO 2 2 85.92 1 2 A PRO 3 2 90.41 1 3 A THR 4 2 86.52 1 4 A LEU 5 2 85.84 1 5 A LEU 6 2 87.07 1 6 A LEU 7 2 87.30 1 7 A LEU 8 2 86.34 1 8 A LEU 9 2 86.90 1 9 A LEU 10 2 88.32 1 10 A LEU 11 2 89.51 1 11 A LEU 12 2 88.95 1 12 A PRO 13 2 93.08 1 13 A PRO 14 2 92.72 1 14 A SER 15 2 92.59 1 15 A LEU 16 2 85.62 1 16 A ALA 17 2 80.12 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 PRO . 2 A 2 A 3 1 n PRO . 3 A 3 A 4 1 n THR . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n PRO . 13 A 13 A 14 1 n PRO . 14 A 14 A 15 1 n SER . 15 A 15 A 16 1 n LEU . 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 ? -1.984 8.455 9.318 1.00 83.55 1 A 1 ATOM 2 C CA . MET A 1 1 ? -2.111 7.867 7.976 1.00 84.44 1 A 1 ATOM 3 C C . MET A 1 1 ? -3.467 7.203 7.803 1.00 86.55 1 A 1 ATOM 4 O O . MET A 1 1 ? -3.952 6.563 8.734 1.00 85.73 1 A 1 ATOM 5 C CB . MET A 1 1 ? -1.021 6.817 7.761 1.00 78.82 1 A 1 ATOM 6 C CG . MET A 1 1 ? 0.371 7.416 7.795 1.00 72.87 1 A 1 ATOM 7 S SD . MET A 1 1 ? 1.623 6.124 7.657 1.00 67.39 1 A 1 ATOM 8 C CE . MET A 1 1 ? 3.099 7.121 7.793 1.00 60.83 1 A 1 ATOM 9 N N . PRO A 1 2 ? -4.064 7.361 6.637 1.00 85.24 2 A 1 ATOM 10 C CA . PRO A 1 2 ? -5.372 6.770 6.358 1.00 89.22 2 A 1 ATOM 11 C C . PRO A 1 2 ? -5.282 5.259 6.148 1.00 90.70 2 A 1 ATOM 12 O O . PRO A 1 2 ? -4.229 4.748 5.761 1.00 88.16 2 A 1 ATOM 13 C CB . PRO A 1 2 ? -5.808 7.474 5.076 1.00 85.68 2 A 1 ATOM 14 C CG . PRO A 1 2 ? -4.539 7.863 4.410 1.00 80.73 2 A 1 ATOM 15 C CD . PRO A 1 2 ? -3.533 8.103 5.507 1.00 81.69 2 A 1 ATOM 16 N N . PRO A 1 3 ? -6.386 4.555 6.378 1.00 91.74 3 A 1 ATOM 17 C CA . PRO A 1 3 ? -6.419 3.099 6.191 1.00 92.27 3 A 1 ATOM 18 C C . PRO A 1 3 ? -6.334 2.707 4.720 1.00 92.99 3 A 1 ATOM 19 O O . PRO A 1 3 ? -5.948 1.586 4.389 1.00 90.22 3 A 1 ATOM 20 C CB . PRO A 1 3 ? -7.766 2.695 6.794 1.00 89.58 3 A 1 ATOM 21 C CG . PRO A 1 3 ? -8.595 3.925 6.694 1.00 86.95 3 A 1 ATOM 22 C CD . PRO A 1 3 ? -7.653 5.093 6.811 1.00 89.09 3 A 1 ATOM 23 N N . THR A 1 4 ? -6.692 3.643 3.861 1.00 88.94 4 A 1 ATOM 24 C CA . THR A 1 4 ? -6.650 3.402 2.418 1.00 89.99 4 A 1 ATOM 25 C C . THR A 1 4 ? -5.228 3.114 1.950 1.00 89.72 4 A 1 ATOM 26 O O . THR A 1 4 ? -5.018 2.315 1.037 1.00 87.21 4 A 1 ATOM 27 C CB . THR A 1 4 ? -7.201 4.615 1.663 1.00 88.19 4 A 1 ATOM 28 O OG1 . THR A 1 4 ? -6.698 5.804 2.231 1.00 81.83 4 A 1 ATOM 29 C CG2 . THR A 1 4 ? -8.715 4.633 1.702 1.00 79.76 4 A 1 ATOM 30 N N . LEU A 1 5 ? -4.282 3.752 2.586 1.00 90.19 5 A 1 ATOM 31 C CA . LEU A 1 5 ? -2.873 3.563 2.239 1.00 89.50 5 A 1 ATOM 32 C C . LEU A 1 5 ? -2.438 2.131 2.525 1.00 90.01 5 A 1 ATOM 33 O O . LEU A 1 5 ? -1.702 1.529 1.741 1.00 87.82 5 A 1 ATOM 34 C CB . LEU A 1 5 ? -2.012 4.542 3.036 1.00 88.05 5 A 1 ATOM 35 C CG . LEU A 1 5 ? -0.550 4.571 2.603 1.00 83.13 5 A 1 ATOM 36 C CD1 . LEU A 1 5 ? -0.408 5.241 1.240 1.00 79.13 5 A 1 ATOM 37 C CD2 . LEU A 1 5 ? 0.289 5.308 3.633 1.00 78.88 5 A 1 ATOM 38 N N . LEU A 1 6 ? -2.891 1.607 3.636 1.00 90.23 6 A 1 ATOM 39 C CA . LEU A 1 6 ? -2.569 0.235 4.025 1.00 89.71 6 A 1 ATOM 40 C C . LEU A 1 6 ? -3.129 -0.749 3.005 1.00 90.15 6 A 1 ATOM 41 O O . LEU A 1 6 ? -2.467 -1.725 2.646 1.00 88.82 6 A 1 ATOM 42 C CB . LEU A 1 6 ? -3.142 -0.054 5.410 1.00 88.99 6 A 1 ATOM 43 C CG . LEU A 1 6 ? -2.678 -1.374 6.002 1.00 84.65 6 A 1 ATOM 44 C CD1 . LEU A 1 6 ? -1.211 -1.291 6.413 1.00 81.96 6 A 1 ATOM 45 C CD2 . LEU A 1 6 ? -3.531 -1.742 7.201 1.00 82.07 6 A 1 ATOM 46 N N . LEU A 1 7 ? -4.329 -0.476 2.559 1.00 90.01 7 A 1 ATOM 47 C CA . LEU A 1 7 ? -4.984 -1.325 1.567 1.00 89.81 7 A 1 ATOM 48 C C . LEU A 1 7 ? -4.204 -1.308 0.255 1.00 90.18 7 A 1 ATOM 49 O O . LEU A 1 7 ? -4.031 -2.344 -0.386 1.00 88.57 7 A 1 ATOM 50 C CB . LEU A 1 7 ? -6.414 -0.842 1.344 1.00 89.21 7 A 1 ATOM 51 C CG . LEU A 1 7 ? -7.263 -1.794 0.514 1.00 84.31 7 A 1 ATOM 52 C CD1 . LEU A 1 7 ? -7.587 -3.053 1.314 1.00 82.89 7 A 1 ATOM 53 C CD2 . LEU A 1 7 ? -8.542 -1.106 0.082 1.00 83.39 7 A 1 ATOM 54 N N . LEU A 1 8 ? -3.741 -0.147 -0.111 1.00 89.06 8 A 1 ATOM 55 C CA . LEU A 1 8 ? -2.961 0.015 -1.338 1.00 88.55 8 A 1 ATOM 56 C C . LEU A 1 8 ? -1.656 -0.767 -1.246 1.00 88.88 8 A 1 ATOM 57 O O . LEU A 1 8 ? -1.231 -1.396 -2.214 1.00 86.94 8 A 1 ATOM 58 C CB . LEU A 1 8 ? -2.678 1.498 -1.569 1.00 88.26 8 A 1 ATOM 59 C CG . LEU A 1 8 ? -2.051 1.808 -2.927 1.00 83.94 8 A 1 ATOM 60 C CD1 . LEU A 1 8 ? -3.087 1.661 -4.040 1.00 82.22 8 A 1 ATOM 61 C CD2 . LEU A 1 8 ? -1.483 3.215 -2.933 1.00 82.83 8 A 1 ATOM 62 N N . LEU A 1 9 ? -1.043 -0.725 -0.088 1.00 88.56 9 A 1 ATOM 63 C CA . LEU A 1 9 ? 0.210 -1.440 0.145 1.00 88.29 9 A 1 ATOM 64 C C . LEU A 1 9 ? 0.010 -2.945 -0.004 1.00 88.19 9 A 1 ATOM 65 O O . LEU A 1 9 ? 0.875 -3.638 -0.542 1.00 86.15 9 A 1 ATOM 66 C CB . LEU A 1 9 ? 0.723 -1.114 1.543 1.00 88.17 9 A 1 ATOM 67 C CG . LEU A 1 9 ? 2.139 -1.613 1.811 1.00 86.21 9 A 1 ATOM 68 C CD1 . LEU A 1 9 ? 3.164 -0.733 1.096 1.00 84.55 9 A 1 ATOM 69 C CD2 . LEU A 1 9 ? 2.413 -1.609 3.306 1.00 85.11 9 A 1 ATOM 70 N N . LEU A 1 10 ? -1.122 -3.419 0.477 1.00 90.13 10 A 1 ATOM 71 C CA . LEU A 1 10 ? -1.452 -4.838 0.389 1.00 89.80 10 A 1 ATOM 72 C C . LEU A 1 10 ? -1.672 -5.256 -1.058 1.00 90.02 10 A 1 ATOM 73 O O . LEU A 1 10 ? -1.266 -6.343 -1.471 1.00 87.30 10 A 1 ATOM 74 C CB . LEU A 1 10 ? -2.708 -5.116 1.220 1.00 89.73 10 A 1 ATOM 75 C CG . LEU A 1 10 ? -2.444 -5.977 2.449 1.00 87.74 10 A 1 ATOM 76 C CD1 . LEU A 1 10 ? -3.549 -5.785 3.473 1.00 85.51 10 A 1 ATOM 77 C CD2 . LEU A 1 10 ? -2.329 -7.439 2.062 1.00 86.34 10 A 1 ATOM 78 N N . LEU A 1 11 ? -2.308 -4.376 -1.806 1.00 91.99 11 A 1 ATOM 79 C CA . LEU A 1 11 ? -2.595 -4.646 -3.209 1.00 91.62 11 A 1 ATOM 80 C C . LEU A 1 11 ? -1.348 -4.487 -4.068 1.00 92.36 11 A 1 ATOM 81 O O . LEU A 1 11 ? -1.256 -5.077 -5.147 1.00 89.58 11 A 1 ATOM 82 C CB . LEU A 1 11 ? -3.690 -3.695 -3.696 1.00 90.89 11 A 1 ATOM 83 C CG . LEU A 1 11 ? -5.095 -4.043 -3.205 1.00 88.51 11 A 1 ATOM 84 C CD1 . LEU A 1 11 ? -6.010 -2.839 -3.332 1.00 85.52 11 A 1 ATOM 85 C CD2 . LEU A 1 11 ? -5.656 -5.211 -4.006 1.00 85.64 11 A 1 ATOM 86 N N . LEU A 1 12 ? -0.418 -3.699 -3.586 1.00 92.02 12 A 1 ATOM 87 C CA . LEU A 1 12 ? 0.818 -3.443 -4.307 1.00 92.42 12 A 1 ATOM 88 C C . LEU A 1 12 ? 1.598 -4.732 -4.537 1.00 93.38 12 A 1 ATOM 89 O O . LEU A 1 12 ? 1.742 -5.543 -3.626 1.00 91.46 12 A 1 ATOM 90 C CB . LEU A 1 12 ? 1.670 -2.445 -3.533 1.00 90.91 12 A 1 ATOM 91 C CG . LEU A 1 12 ? 2.528 -1.550 -4.419 1.00 86.33 12 A 1 ATOM 92 C CD1 . LEU A 1 12 ? 1.709 -0.400 -4.982 1.00 82.77 12 A 1 ATOM 93 C CD2 . LEU A 1 12 ? 3.699 -1.005 -3.621 1.00 82.34 12 A 1 ATOM 94 N N . PRO A 1 13 ? 2.114 -4.923 -5.751 1.00 94.24 13 A 1 ATOM 95 C CA . PRO A 1 13 ? 2.872 -6.127 -6.077 1.00 94.35 13 A 1 ATOM 96 C C . PRO A 1 13 ? 4.259 -6.114 -5.439 1.00 94.80 13 A 1 ATOM 97 O O . PRO A 1 13 ? 4.814 -5.049 -5.169 1.00 92.95 13 A 1 ATOM 98 C CB . PRO A 1 13 ? 2.967 -6.085 -7.603 1.00 92.30 13 A 1 ATOM 99 C CG . PRO A 1 13 ? 2.875 -4.644 -7.947 1.00 90.55 13 A 1 ATOM 100 C CD . PRO A 1 13 ? 1.996 -4.019 -6.896 1.00 92.39 13 A 1 ATOM 101 N N . PRO A 1 14 ? 4.838 -7.292 -5.218 1.00 94.20 14 A 1 ATOM 102 C CA . PRO A 1 14 ? 6.171 -7.399 -4.623 1.00 93.94 14 A 1 ATOM 103 C C . PRO A 1 14 ? 7.266 -6.932 -5.573 1.00 94.72 14 A 1 ATOM 104 O O . PRO A 1 14 ? 8.381 -6.633 -5.146 1.00 92.07 14 A 1 ATOM 105 C CB . PRO A 1 14 ? 6.301 -8.894 -4.329 1.00 91.63 14 A 1 ATOM 106 C CG . PRO A 1 14 ? 5.403 -9.545 -5.323 1.00 90.01 14 A 1 ATOM 107 C CD . PRO A 1 14 ? 4.266 -8.575 -5.561 1.00 92.49 14 A 1 ATOM 108 N N . SER A 1 15 ? 6.934 -6.891 -6.847 1.00 94.88 15 A 1 ATOM 109 C CA . SER A 1 15 ? 7.879 -6.456 -7.874 1.00 94.68 15 A 1 ATOM 110 C C . SER A 1 15 ? 8.363 -5.039 -7.612 1.00 94.45 15 A 1 ATOM 111 O O . SER A 1 15 ? 9.548 -4.735 -7.787 1.00 91.84 15 A 1 ATOM 112 C CB . SER A 1 15 ? 7.230 -6.537 -9.255 1.00 93.06 15 A 1 ATOM 113 O OG . SER A 1 15 ? 8.084 -6.019 -10.242 1.00 86.65 15 A 1 ATOM 114 N N . LEU A 1 16 ? 7.441 -4.190 -7.198 1.00 91.61 16 A 1 ATOM 115 C CA . LEU A 1 16 ? 7.766 -2.802 -6.909 1.00 90.52 16 A 1 ATOM 116 C C . LEU A 1 16 ? 8.549 -2.681 -5.608 1.00 90.37 16 A 1 ATOM 117 O O . LEU A 1 16 ? 9.533 -1.939 -5.540 1.00 87.82 16 A 1 ATOM 118 C CB . LEU A 1 16 ? 6.482 -1.974 -6.827 1.00 87.98 16 A 1 ATOM 119 C CG . LEU A 1 16 ? 6.724 -0.474 -6.761 1.00 83.15 16 A 1 ATOM 120 C CD1 . LEU A 1 16 ? 7.137 0.062 -8.121 1.00 77.79 16 A 1 ATOM 121 C CD2 . LEU A 1 16 ? 5.467 0.239 -6.290 1.00 75.68 16 A 1 ATOM 122 N N . ALA A 1 17 ? 8.093 -3.395 -4.600 1.00 87.60 17 A 1 ATOM 123 C CA . ALA A 1 17 ? 8.736 -3.374 -3.284 1.00 84.39 17 A 1 ATOM 124 C C . ALA A 1 17 ? 10.071 -4.100 -3.337 1.00 80.43 17 A 1 ATOM 125 O O . ALA A 1 17 ? 11.108 -3.483 -3.014 1.00 76.43 17 A 1 ATOM 126 C CB . ALA A 1 17 ? 7.821 -4.011 -2.250 1.00 79.02 17 A 1 ATOM 127 O OXT . ALA A 1 17 ? 10.068 -5.265 -3.701 1.00 72.86 17 A 1 #