# 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_spkb31187 # _entry.id spkb31187 # 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" "C2 H5 N O2" 75.067 GLY y GLYCINE C(C(=O)O)N ? "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" "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 VAL 3 1 n THR 4 1 n ALA 5 1 n ALA 6 1 n PHE 7 1 n ALA 8 1 n GLY 9 1 n LEU 10 1 n LEU 11 1 n VAL 12 1 n THR 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 15:59:52)" _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 94.73 _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 87.69 1 1 A LYS 2 2 90.17 1 2 A VAL 3 2 95.94 1 3 A THR 4 2 94.60 1 4 A ALA 5 2 96.69 1 5 A ALA 6 2 97.43 1 6 A PHE 7 2 95.37 1 7 A ALA 8 2 97.42 1 8 A GLY 9 2 97.21 1 9 A LEU 10 2 95.74 1 10 A LEU 11 2 95.14 1 11 A VAL 12 2 97.25 1 12 A THR 13 2 96.52 1 13 A ALA 14 2 97.87 1 14 A LEU 15 2 94.62 1 15 A ALA 16 2 91.29 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 VAL . 3 A 3 A 4 1 n THR . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n ALA . 6 A 6 A 7 1 n PHE . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n GLY . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n VAL . 12 A 12 A 13 1 n THR . 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 ? 1.448 11.300 2.592 1.00 91.04 1 A 1 ATOM 2 C CA . MET A 1 1 ? 0.669 10.156 2.063 1.00 92.73 1 A 1 ATOM 3 C C . MET A 1 1 ? 1.138 8.830 2.666 1.00 94.19 1 A 1 ATOM 4 O O . MET A 1 1 ? 1.625 7.956 1.967 1.00 91.74 1 A 1 ATOM 5 C CB . MET A 1 1 ? 0.835 10.087 0.550 1.00 89.22 1 A 1 ATOM 6 C CG . MET A 1 1 ? 0.281 11.313 -0.133 1.00 86.40 1 A 1 ATOM 7 S SD . MET A 1 1 ? 0.396 11.166 -1.918 1.00 83.07 1 A 1 ATOM 8 C CE . MET A 1 1 ? 1.430 12.567 -2.276 1.00 73.14 1 A 1 ATOM 9 N N . LYS A 1 2 ? 0.994 8.701 3.962 1.00 94.38 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 1.410 7.462 4.630 1.00 95.90 2 A 1 ATOM 11 C C . LYS A 1 2 ? 0.323 6.393 4.512 1.00 96.52 2 A 1 ATOM 12 O O . LYS A 1 2 ? 0.620 5.201 4.489 1.00 96.14 2 A 1 ATOM 13 C CB . LYS A 1 2 ? 1.722 7.756 6.096 1.00 94.71 2 A 1 ATOM 14 C CG . LYS A 1 2 ? 0.571 8.454 6.808 1.00 89.35 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 1.075 9.091 8.091 1.00 87.21 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 0.006 9.934 8.741 1.00 81.53 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 0.637 10.957 9.610 1.00 75.83 2 A 1 ATOM 18 N N . VAL A 1 3 ? -0.913 6.809 4.429 1.00 96.68 3 A 1 ATOM 19 C CA . VAL A 1 3 ? -2.042 5.882 4.288 1.00 97.24 3 A 1 ATOM 20 C C . VAL A 1 3 ? -1.993 5.199 2.926 1.00 97.84 3 A 1 ATOM 21 O O . VAL A 1 3 ? -2.199 3.989 2.807 1.00 97.31 3 A 1 ATOM 22 C CB . VAL A 1 3 ? -3.372 6.630 4.458 1.00 96.35 3 A 1 ATOM 23 C CG1 . VAL A 1 3 ? -4.531 5.662 4.341 1.00 93.13 3 A 1 ATOM 24 C CG2 . VAL A 1 3 ? -3.408 7.335 5.806 1.00 93.02 3 A 1 ATOM 25 N N . THR A 1 4 ? -1.714 5.977 1.908 1.00 95.40 4 A 1 ATOM 26 C CA . THR A 1 4 ? -1.637 5.452 0.544 1.00 95.68 4 A 1 ATOM 27 C C . THR A 1 4 ? -0.497 4.445 0.427 1.00 96.36 4 A 1 ATOM 28 O O . THR A 1 4 ? -0.611 3.434 -0.264 1.00 96.43 4 A 1 ATOM 29 C CB . THR A 1 4 ? -1.405 6.598 -0.443 1.00 95.56 4 A 1 ATOM 30 O OG1 . THR A 1 4 ? -2.243 7.695 -0.100 1.00 92.38 4 A 1 ATOM 31 C CG2 . THR A 1 4 ? -1.736 6.148 -1.856 1.00 90.39 4 A 1 ATOM 32 N N . ALA A 1 5 ? 0.594 4.711 1.101 1.00 96.77 5 A 1 ATOM 33 C CA . ALA A 1 5 ? 1.756 3.824 1.067 1.00 96.82 5 A 1 ATOM 34 C C . ALA A 1 5 ? 1.403 2.453 1.640 1.00 97.24 5 A 1 ATOM 35 O O . ALA A 1 5 ? 1.812 1.424 1.112 1.00 96.60 5 A 1 ATOM 36 C CB . ALA A 1 5 ? 2.888 4.451 1.866 1.00 96.01 5 A 1 ATOM 37 N N . ALA A 1 6 ? 0.652 2.446 2.717 1.00 97.27 6 A 1 ATOM 38 C CA . ALA A 1 6 ? 0.235 1.196 3.352 1.00 97.45 6 A 1 ATOM 39 C C . ALA A 1 6 ? -0.672 0.396 2.424 1.00 97.95 6 A 1 ATOM 40 O O . ALA A 1 6 ? -0.560 -0.824 2.328 1.00 97.48 6 A 1 ATOM 41 C CB . ALA A 1 6 ? -0.484 1.508 4.654 1.00 97.01 6 A 1 ATOM 42 N N . PHE A 1 7 ? -1.562 1.096 1.748 1.00 97.56 7 A 1 ATOM 43 C CA . PHE A 1 7 ? -2.490 0.457 0.815 1.00 97.56 7 A 1 ATOM 44 C C . PHE A 1 7 ? -1.730 -0.176 -0.341 1.00 97.94 7 A 1 ATOM 45 O O . PHE A 1 7 ? -1.971 -1.326 -0.707 1.00 97.70 7 A 1 ATOM 46 C CB . PHE A 1 7 ? -3.472 1.497 0.282 1.00 97.22 7 A 1 ATOM 47 C CG . PHE A 1 7 ? -4.890 1.182 0.679 1.00 95.62 7 A 1 ATOM 48 C CD1 . PHE A 1 7 ? -5.519 0.053 0.188 1.00 93.62 7 A 1 ATOM 49 C CD2 . PHE A 1 7 ? -5.581 2.024 1.542 1.00 93.81 7 A 1 ATOM 50 C CE1 . PHE A 1 7 ? -6.828 -0.245 0.551 1.00 92.78 7 A 1 ATOM 51 C CE2 . PHE A 1 7 ? -6.889 1.740 1.909 1.00 92.57 7 A 1 ATOM 52 C CZ . PHE A 1 7 ? -7.515 0.602 1.414 1.00 92.66 7 A 1 ATOM 53 N N . ALA A 1 8 ? -0.815 0.566 -0.907 1.00 97.44 8 A 1 ATOM 54 C CA . ALA A 1 8 ? -0.017 0.080 -2.031 1.00 97.42 8 A 1 ATOM 55 C C . ALA A 1 8 ? 0.849 -1.098 -1.607 1.00 97.88 8 A 1 ATOM 56 O O . ALA A 1 8 ? 0.981 -2.076 -2.335 1.00 97.52 8 A 1 ATOM 57 C CB . ALA A 1 8 ? 0.851 1.214 -2.555 1.00 96.83 8 A 1 ATOM 58 N N . GLY A 1 9 ? 1.432 -1.011 -0.431 1.00 96.95 9 A 1 ATOM 59 C CA . GLY A 1 9 ? 2.280 -2.086 0.075 1.00 96.82 9 A 1 ATOM 60 C C . GLY A 1 9 ? 1.509 -3.376 0.271 1.00 97.64 9 A 1 ATOM 61 O O . GLY A 1 9 ? 1.964 -4.449 -0.106 1.00 97.42 9 A 1 ATOM 62 N N . LEU A 1 10 ? 0.343 -3.269 0.869 1.00 97.54 10 A 1 ATOM 63 C CA . LEU A 1 10 ? -0.498 -4.444 1.112 1.00 97.66 10 A 1 ATOM 64 C C . LEU A 1 10 ? -0.960 -5.072 -0.195 1.00 98.20 10 A 1 ATOM 65 O O . LEU A 1 10 ? -0.906 -6.291 -0.359 1.00 97.80 10 A 1 ATOM 66 C CB . LEU A 1 10 ? -1.707 -4.021 1.944 1.00 97.27 10 A 1 ATOM 67 C CG . LEU A 1 10 ? -1.412 -4.067 3.441 1.00 93.80 10 A 1 ATOM 68 C CD1 . LEU A 1 10 ? -2.325 -3.123 4.200 1.00 91.69 10 A 1 ATOM 69 C CD2 . LEU A 1 10 ? -1.585 -5.492 3.956 1.00 91.97 10 A 1 ATOM 70 N N . LEU A 1 11 ? -1.412 -4.247 -1.109 1.00 96.74 11 A 1 ATOM 71 C CA . LEU A 1 11 ? -1.889 -4.735 -2.404 1.00 96.88 11 A 1 ATOM 72 C C . LEU A 1 11 ? -0.755 -5.338 -3.219 1.00 97.64 11 A 1 ATOM 73 O O . LEU A 1 11 ? -0.897 -6.417 -3.791 1.00 97.61 11 A 1 ATOM 74 C CB . LEU A 1 11 ? -2.528 -3.577 -3.168 1.00 96.61 11 A 1 ATOM 75 C CG . LEU A 1 11 ? -3.950 -3.285 -2.699 1.00 93.62 11 A 1 ATOM 76 C CD1 . LEU A 1 11 ? -4.367 -1.881 -3.105 1.00 91.31 11 A 1 ATOM 77 C CD2 . LEU A 1 11 ? -4.909 -4.308 -3.312 1.00 90.74 11 A 1 ATOM 78 N N . VAL A 1 12 ? 0.357 -4.657 -3.271 1.00 97.70 12 A 1 ATOM 79 C CA . VAL A 1 12 ? 1.514 -5.134 -4.038 1.00 97.88 12 A 1 ATOM 80 C C . VAL A 1 12 ? 2.041 -6.435 -3.448 1.00 98.26 12 A 1 ATOM 81 O O . VAL A 1 12 ? 2.371 -7.373 -4.173 1.00 98.09 12 A 1 ATOM 82 C CB . VAL A 1 12 ? 2.617 -4.065 -4.045 1.00 97.36 12 A 1 ATOM 83 C CG1 . VAL A 1 12 ? 3.882 -4.606 -4.694 1.00 95.63 12 A 1 ATOM 84 C CG2 . VAL A 1 12 ? 2.142 -2.837 -4.809 1.00 95.81 12 A 1 ATOM 85 N N . THR A 1 13 ? 2.125 -6.497 -2.139 1.00 97.84 13 A 1 ATOM 86 C CA . THR A 1 13 ? 2.627 -7.693 -1.460 1.00 97.65 13 A 1 ATOM 87 C C . THR A 1 13 ? 1.700 -8.874 -1.722 1.00 98.09 13 A 1 ATOM 88 O O . THR A 1 13 ? 2.157 -9.985 -1.993 1.00 97.86 13 A 1 ATOM 89 C CB . THR A 1 13 ? 2.720 -7.444 0.046 1.00 97.03 13 A 1 ATOM 90 O OG1 . THR A 1 13 ? 3.568 -6.324 0.280 1.00 94.02 13 A 1 ATOM 91 C CG2 . THR A 1 13 ? 3.315 -8.648 0.759 1.00 93.17 13 A 1 ATOM 92 N N . ALA A 1 14 ? 0.413 -8.649 -1.626 1.00 97.98 14 A 1 ATOM 93 C CA . ALA A 1 14 ? -0.572 -9.703 -1.859 1.00 97.94 14 A 1 ATOM 94 C C . ALA A 1 14 ? -0.555 -10.136 -3.317 1.00 98.19 14 A 1 ATOM 95 O O . ALA A 1 14 ? -0.637 -11.325 -3.622 1.00 97.69 14 A 1 ATOM 96 C CB . ALA A 1 14 ? -1.958 -9.203 -1.477 1.00 97.57 14 A 1 ATOM 97 N N . LEU A 1 15 ? -0.450 -9.172 -4.201 1.00 97.15 15 A 1 ATOM 98 C CA . LEU A 1 15 ? -0.408 -9.444 -5.641 1.00 97.07 15 A 1 ATOM 99 C C . LEU A 1 15 ? 0.831 -10.256 -5.986 1.00 97.55 15 A 1 ATOM 100 O O . LEU A 1 15 ? 0.756 -11.249 -6.712 1.00 96.94 15 A 1 ATOM 101 C CB . LEU A 1 15 ? -0.397 -8.118 -6.406 1.00 96.42 15 A 1 ATOM 102 C CG . LEU A 1 15 ? -0.863 -8.264 -7.845 1.00 92.77 15 A 1 ATOM 103 C CD1 . LEU A 1 15 ? -2.050 -7.355 -8.115 1.00 90.16 15 A 1 ATOM 104 C CD2 . LEU A 1 15 ? 0.267 -7.933 -8.802 1.00 88.88 15 A 1 ATOM 105 N N . ALA A 1 16 ? 1.968 -9.820 -5.442 1.00 95.64 16 A 1 ATOM 106 C CA . ALA A 1 16 ? 3.246 -10.508 -5.675 1.00 94.58 16 A 1 ATOM 107 C C . ALA A 1 16 ? 3.433 -10.835 -7.153 1.00 93.63 16 A 1 ATOM 108 O O . ALA A 1 16 ? 3.173 -11.967 -7.576 1.00 90.44 16 A 1 ATOM 109 C CB . ALA A 1 16 ? 3.309 -11.779 -4.848 1.00 90.64 16 A 1 ATOM 110 O OXT . ALA A 1 16 ? 3.869 -9.915 -7.879 1.00 82.82 16 A 1 #