# 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_spkb31261 # _entry.id spkb31261 # 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" "C5 H10 N2 O3" 146.144 GLN y GLUTAMINE C(CC(=O)N)[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" "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" "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 GLN 2 1 n TYR 3 1 n MET 4 1 n THR 5 1 n ILE 6 1 n VAL 7 1 n ALA 8 1 n PHE 9 1 n LEU 10 1 n ALA 11 1 n ALA 12 1 n THR 13 1 n VAL 14 1 n ALA 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 @ 2025-07-13 15:06:33)" _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 94.55 _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 88.68 1 1 A GLN 2 2 89.59 1 2 A TYR 3 2 92.31 1 3 A MET 4 2 92.00 1 4 A THR 5 2 95.25 1 5 A ILE 6 2 96.07 1 6 A VAL 7 2 96.27 1 7 A ALA 8 2 97.82 1 8 A PHE 9 2 95.87 1 9 A LEU 10 2 95.59 1 10 A ALA 11 2 97.56 1 11 A ALA 12 2 97.97 1 12 A THR 13 2 96.15 1 13 A VAL 14 2 96.43 1 14 A ALA 15 2 97.01 1 15 A ALA 16 2 94.74 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 GLN . 2 A 2 A 3 1 n TYR . 3 A 3 A 4 1 n MET . 4 A 4 A 5 1 n THR . 5 A 5 A 6 1 n ILE . 6 A 6 A 7 1 n VAL . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n PHE . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n THR . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n ALA . 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 ? -4.916 -6.952 -3.945 1.00 92.49 1 A 1 ATOM 2 C CA . MET A 1 1 ? -3.744 -6.296 -4.557 1.00 93.68 1 A 1 ATOM 3 C C . MET A 1 1 ? -2.720 -5.919 -3.486 1.00 94.28 1 A 1 ATOM 4 O O . MET A 1 1 ? -3.073 -5.346 -2.459 1.00 92.89 1 A 1 ATOM 5 C CB . MET A 1 1 ? -4.180 -5.034 -5.290 1.00 90.56 1 A 1 ATOM 6 C CG . MET A 1 1 ? -5.104 -5.327 -6.466 1.00 87.22 1 A 1 ATOM 7 S SD . MET A 1 1 ? -4.234 -6.110 -7.823 1.00 84.26 1 A 1 ATOM 8 C CE . MET A 1 1 ? -5.537 -6.179 -9.038 1.00 74.07 1 A 1 ATOM 9 N N . GLN A 1 2 ? -1.467 -6.236 -3.732 1.00 93.40 2 A 1 ATOM 10 C CA . GLN A 1 2 ? -0.394 -5.911 -2.792 1.00 95.12 2 A 1 ATOM 11 C C . GLN A 1 2 ? -0.210 -4.402 -2.677 1.00 96.31 2 A 1 ATOM 12 O O . GLN A 1 2 ? 0.342 -3.913 -1.692 1.00 94.95 2 A 1 ATOM 13 C CB . GLN A 1 2 ? 0.908 -6.554 -3.256 1.00 93.37 2 A 1 ATOM 14 C CG . GLN A 1 2 ? 0.891 -8.066 -3.124 1.00 88.52 2 A 1 ATOM 15 C CD . GLN A 1 2 ? 2.210 -8.683 -3.535 1.00 86.53 2 A 1 ATOM 16 O OE1 . GLN A 1 2 ? 3.100 -7.994 -4.023 1.00 79.78 2 A 1 ATOM 17 N NE2 . GLN A 1 2 ? 2.358 -9.978 -3.346 1.00 78.34 2 A 1 ATOM 18 N N . TYR A 1 3 ? -0.675 -3.675 -3.680 1.00 94.80 3 A 1 ATOM 19 C CA . TYR A 1 3 ? -0.564 -2.221 -3.678 1.00 95.88 3 A 1 ATOM 20 C C . TYR A 1 3 ? -1.344 -1.617 -2.518 1.00 96.95 3 A 1 ATOM 21 O O . TYR A 1 3 ? -0.999 -0.548 -2.013 1.00 96.54 3 A 1 ATOM 22 C CB . TYR A 1 3 ? -1.086 -1.664 -5.005 1.00 94.98 3 A 1 ATOM 23 C CG . TYR A 1 3 ? -0.244 -2.106 -6.180 1.00 92.17 3 A 1 ATOM 24 C CD1 . TYR A 1 3 ? 1.077 -1.677 -6.294 1.00 90.89 3 A 1 ATOM 25 C CD2 . TYR A 1 3 ? -0.762 -2.941 -7.162 1.00 89.50 3 A 1 ATOM 26 C CE1 . TYR A 1 3 ? 1.862 -2.079 -7.365 1.00 89.47 3 A 1 ATOM 27 C CE2 . TYR A 1 3 ? 0.020 -3.347 -8.238 1.00 89.00 3 A 1 ATOM 28 C CZ . TYR A 1 3 ? 1.329 -2.910 -8.334 1.00 89.06 3 A 1 ATOM 29 O OH . TYR A 1 3 ? 2.102 -3.307 -9.395 1.00 88.50 3 A 1 ATOM 30 N N . MET A 1 4 ? -2.389 -2.308 -2.067 1.00 95.36 4 A 1 ATOM 31 C CA . MET A 1 4 ? -3.199 -1.831 -0.945 1.00 96.38 4 A 1 ATOM 32 C C . MET A 1 4 ? -2.347 -1.703 0.315 1.00 97.36 4 A 1 ATOM 33 O O . MET A 1 4 ? -2.458 -0.738 1.065 1.00 96.75 4 A 1 ATOM 34 C CB . MET A 1 4 ? -4.367 -2.792 -0.701 1.00 95.49 4 A 1 ATOM 35 C CG . MET A 1 4 ? -5.689 -2.177 -1.129 1.00 92.31 4 A 1 ATOM 36 S SD . MET A 1 4 ? -6.197 -0.898 0.010 1.00 85.99 4 A 1 ATOM 37 C CE . MET A 1 4 ? -7.529 -0.144 -0.931 1.00 76.39 4 A 1 ATOM 38 N N . THR A 1 5 ? -1.491 -2.680 0.533 1.00 95.97 5 A 1 ATOM 39 C CA . THR A 1 5 ? -0.604 -2.670 1.693 1.00 96.67 5 A 1 ATOM 40 C C . THR A 1 5 ? 0.411 -1.536 1.575 1.00 97.39 5 A 1 ATOM 41 O O . THR A 1 5 ? 0.731 -0.865 2.558 1.00 97.17 5 A 1 ATOM 42 C CB . THR A 1 5 ? 0.138 -4.005 1.816 1.00 96.22 5 A 1 ATOM 43 O OG1 . THR A 1 5 ? -0.806 -5.074 1.835 1.00 92.42 5 A 1 ATOM 44 C CG2 . THR A 1 5 ? 0.973 -4.041 3.080 1.00 90.94 5 A 1 ATOM 45 N N . ILE A 1 6 ? 0.895 -1.321 0.375 1.00 97.48 6 A 1 ATOM 46 C CA . ILE A 1 6 ? 1.867 -0.261 0.126 1.00 97.61 6 A 1 ATOM 47 C C . ILE A 1 6 ? 1.234 1.102 0.377 1.00 97.97 6 A 1 ATOM 48 O O . ILE A 1 6 ? 1.866 1.998 0.942 1.00 97.81 6 A 1 ATOM 49 C CB . ILE A 1 6 ? 2.398 -0.345 -1.312 1.00 97.36 6 A 1 ATOM 50 C CG1 . ILE A 1 6 ? 3.116 -1.684 -1.524 1.00 95.27 6 A 1 ATOM 51 C CG2 . ILE A 1 6 ? 3.350 0.812 -1.591 1.00 94.91 6 A 1 ATOM 52 C CD1 . ILE A 1 6 ? 3.488 -1.930 -2.970 1.00 90.16 6 A 1 ATOM 53 N N . VAL A 1 7 ? -0.013 1.250 -0.033 1.00 96.67 7 A 1 ATOM 54 C CA . VAL A 1 7 ? -0.732 2.507 0.158 1.00 96.95 7 A 1 ATOM 55 C C . VAL A 1 7 ? -0.888 2.802 1.646 1.00 97.46 7 A 1 ATOM 56 O O . VAL A 1 7 ? -0.735 3.942 2.085 1.00 97.53 7 A 1 ATOM 57 C CB . VAL A 1 7 ? -2.115 2.451 -0.519 1.00 96.53 7 A 1 ATOM 58 C CG1 . VAL A 1 7 ? -2.939 3.683 -0.168 1.00 94.33 7 A 1 ATOM 59 C CG2 . VAL A 1 7 ? -1.948 2.356 -2.029 1.00 94.44 7 A 1 ATOM 60 N N . ALA A 1 8 ? -1.198 1.769 2.422 1.00 97.64 8 A 1 ATOM 61 C CA . ALA A 1 8 ? -1.366 1.926 3.861 1.00 97.82 8 A 1 ATOM 62 C C . ALA A 1 8 ? -0.059 2.386 4.506 1.00 98.14 8 A 1 ATOM 63 O O . ALA A 1 8 ? -0.057 3.253 5.381 1.00 97.92 8 A 1 ATOM 64 C CB . ALA A 1 8 ? -1.822 0.606 4.469 1.00 97.56 8 A 1 ATOM 65 N N . PHE A 1 9 ? 1.034 1.807 4.062 1.00 97.09 9 A 1 ATOM 66 C CA . PHE A 1 9 ? 2.350 2.171 4.580 1.00 97.19 9 A 1 ATOM 67 C C . PHE A 1 9 ? 2.686 3.618 4.225 1.00 97.76 9 A 1 ATOM 68 O O . PHE A 1 9 ? 3.155 4.387 5.068 1.00 97.62 9 A 1 ATOM 69 C CB . PHE A 1 9 ? 3.409 1.231 4.000 1.00 96.91 9 A 1 ATOM 70 C CG . PHE A 1 9 ? 4.814 1.668 4.330 1.00 96.14 9 A 1 ATOM 71 C CD1 . PHE A 1 9 ? 5.293 1.563 5.629 1.00 94.94 9 A 1 ATOM 72 C CD2 . PHE A 1 9 ? 5.641 2.182 3.347 1.00 95.17 9 A 1 ATOM 73 C CE1 . PHE A 1 9 ? 6.581 1.972 5.942 1.00 94.10 9 A 1 ATOM 74 C CE2 . PHE A 1 9 ? 6.934 2.596 3.654 1.00 93.96 9 A 1 ATOM 75 C CZ . PHE A 1 9 ? 7.403 2.492 4.951 1.00 93.70 9 A 1 ATOM 76 N N . LEU A 1 10 ? 2.435 3.971 2.983 1.00 96.80 10 A 1 ATOM 77 C CA . LEU A 1 10 ? 2.711 5.327 2.520 1.00 96.93 10 A 1 ATOM 78 C C . LEU A 1 10 ? 1.837 6.335 3.256 1.00 97.65 10 A 1 ATOM 79 O O . LEU A 1 10 ? 2.297 7.413 3.632 1.00 97.71 10 A 1 ATOM 80 C CB . LEU A 1 10 ? 2.458 5.419 1.016 1.00 96.66 10 A 1 ATOM 81 C CG . LEU A 1 10 ? 2.836 6.770 0.414 1.00 93.41 10 A 1 ATOM 82 C CD1 . LEU A 1 10 ? 4.334 7.003 0.520 1.00 92.59 10 A 1 ATOM 83 C CD2 . LEU A 1 10 ? 2.396 6.837 -1.038 1.00 92.94 10 A 1 ATOM 84 N N . ALA A 1 11 ? 0.572 5.979 3.460 1.00 97.63 11 A 1 ATOM 85 C CA . ALA A 1 11 ? -0.371 6.850 4.155 1.00 97.59 11 A 1 ATOM 86 C C . ALA A 1 11 ? 0.092 7.112 5.582 1.00 97.93 11 A 1 ATOM 87 O O . ALA A 1 11 ? -0.019 8.230 6.085 1.00 97.54 11 A 1 ATOM 88 C CB . ALA A 1 11 ? -1.755 6.207 4.162 1.00 97.12 11 A 1 ATOM 89 N N . ALA A 1 12 ? 0.609 6.081 6.238 1.00 98.10 12 A 1 ATOM 90 C CA . ALA A 1 12 ? 1.093 6.210 7.609 1.00 98.08 12 A 1 ATOM 91 C C . ALA A 1 12 ? 2.281 7.165 7.671 1.00 98.29 12 A 1 ATOM 92 O O . ALA A 1 12 ? 2.410 7.952 8.607 1.00 97.71 12 A 1 ATOM 93 C CB . ALA A 1 12 ? 1.484 4.842 8.148 1.00 97.68 12 A 1 ATOM 94 N N . THR A 1 13 ? 3.132 7.095 6.665 1.00 97.64 13 A 1 ATOM 95 C CA . THR A 1 13 ? 4.309 7.961 6.602 1.00 97.50 13 A 1 ATOM 96 C C . THR A 1 13 ? 3.905 9.420 6.409 1.00 97.77 13 A 1 ATOM 97 O O . THR A 1 13 ? 4.473 10.318 7.031 1.00 96.95 13 A 1 ATOM 98 C CB . THR A 1 13 ? 5.220 7.535 5.449 1.00 96.53 13 A 1 ATOM 99 O OG1 . THR A 1 13 ? 5.559 6.156 5.600 1.00 93.40 13 A 1 ATOM 100 C CG2 . THR A 1 13 ? 6.495 8.360 5.446 1.00 93.28 13 A 1 ATOM 101 N N . VAL A 1 14 ? 2.927 9.644 5.546 1.00 97.77 14 A 1 ATOM 102 C CA . VAL A 1 14 ? 2.446 10.997 5.271 1.00 97.71 14 A 1 ATOM 103 C C . VAL A 1 14 ? 1.640 11.544 6.444 1.00 98.05 14 A 1 ATOM 104 O O . VAL A 1 14 ? 1.663 12.748 6.721 1.00 97.62 14 A 1 ATOM 105 C CB . VAL A 1 14 ? 1.583 11.010 3.999 1.00 96.71 14 A 1 ATOM 106 C CG1 . VAL A 1 14 ? 1.022 12.399 3.749 1.00 93.39 14 A 1 ATOM 107 C CG2 . VAL A 1 14 ? 2.411 10.553 2.809 1.00 93.75 14 A 1 ATOM 108 N N . ALA A 1 15 ? 0.921 10.660 7.129 1.00 97.41 15 A 1 ATOM 109 C CA . ALA A 1 15 ? 0.076 11.052 8.257 1.00 97.28 15 A 1 ATOM 110 C C . ALA A 1 15 ? 0.893 11.365 9.507 1.00 97.45 15 A 1 ATOM 111 O O . ALA A 1 15 ? 0.341 11.835 10.502 1.00 96.64 15 A 1 ATOM 112 C CB . ALA A 1 15 ? -0.935 9.943 8.563 1.00 96.28 15 A 1 ATOM 113 N N . ALA A 1 16 ? 2.189 11.132 9.467 1.00 97.38 16 A 1 ATOM 114 C CA . ALA A 1 16 ? 3.065 11.358 10.623 1.00 96.81 16 A 1 ATOM 115 C C . ALA A 1 16 ? 3.192 12.845 10.950 1.00 96.43 16 A 1 ATOM 116 O O . ALA A 1 16 ? 4.311 13.351 11.087 1.00 94.05 16 A 1 ATOM 117 C CB . ALA A 1 16 ? 4.432 10.741 10.357 1.00 95.08 16 A 1 ATOM 118 O OXT . ALA A 1 16 ? 2.148 13.517 11.104 1.00 88.67 16 A 1 #