# 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_spkb12597 # _entry.id spkb12597 # 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" "C4 H8 N2 O3" 132.118 ASN y ASPARAGINE C([C@@H](C(=O)O)N)C(=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" "C3 H7 N O3" 105.093 SER y SERINE C([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 ILE 2 1 n LEU 3 1 n ASN 4 1 n LEU 5 1 n ILE 6 1 n ILE 7 1 n LEU 8 1 n LEU 9 1 n ALA 10 1 n ILE 11 1 n SER 12 1 n ILE 13 1 n VAL 14 1 n ALA 15 1 n SER 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 01:11:29)" _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 97.08 _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 92.26 1 1 A ILE 2 2 96.41 1 2 A LEU 3 2 97.35 1 3 A ASN 4 2 97.00 1 4 A LEU 5 2 97.09 1 5 A ILE 6 2 98.18 1 6 A ILE 7 2 98.29 1 7 A LEU 8 2 97.12 1 8 A LEU 9 2 96.46 1 9 A ALA 10 2 98.72 1 10 A ILE 11 2 98.05 1 11 A SER 12 2 97.89 1 12 A ILE 13 2 98.04 1 13 A VAL 14 2 98.23 1 14 A ALA 15 2 98.52 1 15 A SER 16 2 96.93 1 16 A ALA 17 2 94.73 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 ILE . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n ASN . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n ILE . 6 A 6 A 7 1 n ILE . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n ALA . 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 ALA . 15 A 15 A 16 1 n SER . 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 ? 8.434 8.336 -1.011 1.00 96.34 1 A 1 ATOM 2 C CA . MET A 1 1 ? 9.213 7.090 -0.904 1.00 96.91 1 A 1 ATOM 3 C C . MET A 1 1 ? 8.452 5.920 -1.507 1.00 97.28 1 A 1 ATOM 4 O O . MET A 1 1 ? 7.227 5.837 -1.379 1.00 96.47 1 A 1 ATOM 5 C CB . MET A 1 1 ? 9.533 6.787 0.559 1.00 94.61 1 A 1 ATOM 6 C CG . MET A 1 1 ? 10.461 7.803 1.191 1.00 89.20 1 A 1 ATOM 7 S SD . MET A 1 1 ? 10.829 7.450 2.912 1.00 87.65 1 A 1 ATOM 8 C CE . MET A 1 1 ? 9.328 8.000 3.701 1.00 79.63 1 A 1 ATOM 9 N N . ILE A 1 2 ? 9.179 5.012 -2.161 1.00 97.33 2 A 1 ATOM 10 C CA . ILE A 1 2 ? 8.574 3.850 -2.819 1.00 98.13 2 A 1 ATOM 11 C C . ILE A 1 2 ? 7.824 2.967 -1.829 1.00 98.54 2 A 1 ATOM 12 O O . ILE A 1 2 ? 6.697 2.540 -2.088 1.00 98.41 2 A 1 ATOM 13 C CB . ILE A 1 2 ? 9.648 3.015 -3.538 1.00 97.65 2 A 1 ATOM 14 C CG1 . ILE A 1 2 ? 10.334 3.861 -4.618 1.00 95.28 2 A 1 ATOM 15 C CG2 . ILE A 1 2 ? 9.035 1.766 -4.155 1.00 94.48 2 A 1 ATOM 16 C CD1 . ILE A 1 2 ? 9.378 4.357 -5.689 1.00 91.46 2 A 1 ATOM 17 N N . LEU A 1 3 ? 8.448 2.678 -0.698 1.00 98.58 3 A 1 ATOM 18 C CA . LEU A 1 3 ? 7.831 1.824 0.314 1.00 98.61 3 A 1 ATOM 19 C C . LEU A 1 3 ? 6.516 2.418 0.806 1.00 98.71 3 A 1 ATOM 20 O O . LEU A 1 3 ? 5.531 1.704 0.997 1.00 98.60 3 A 1 ATOM 21 C CB . LEU A 1 3 ? 8.793 1.621 1.486 1.00 98.43 3 A 1 ATOM 22 C CG . LEU A 1 3 ? 8.277 0.719 2.610 1.00 96.58 3 A 1 ATOM 23 C CD1 . LEU A 1 3 ? 7.921 -0.657 2.062 1.00 94.81 3 A 1 ATOM 24 C CD2 . LEU A 1 3 ? 9.330 0.600 3.697 1.00 94.52 3 A 1 ATOM 25 N N . ASN A 1 4 ? 6.486 3.724 0.997 1.00 98.55 4 A 1 ATOM 26 C CA . ASN A 1 4 ? 5.297 4.427 1.455 1.00 98.64 4 A 1 ATOM 27 C C . ASN A 1 4 ? 4.164 4.277 0.446 1.00 98.73 4 A 1 ATOM 28 O O . ASN A 1 4 ? 3.014 4.031 0.809 1.00 98.60 4 A 1 ATOM 29 C CB . ASN A 1 4 ? 5.619 5.912 1.659 1.00 98.44 4 A 1 ATOM 30 C CG . ASN A 1 4 ? 4.683 6.574 2.650 1.00 96.46 4 A 1 ATOM 31 O OD1 . ASN A 1 4 ? 4.885 7.731 3.024 1.00 93.51 4 A 1 ATOM 32 N ND2 . ASN A 1 4 ? 3.673 5.864 3.109 1.00 93.03 4 A 1 ATOM 33 N N . LEU A 1 5 ? 4.488 4.402 -0.837 1.00 98.72 5 A 1 ATOM 34 C CA . LEU A 1 5 ? 3.506 4.268 -1.906 1.00 98.75 5 A 1 ATOM 35 C C . LEU A 1 5 ? 2.981 2.840 -1.997 1.00 98.82 5 A 1 ATOM 36 O O . LEU A 1 5 ? 1.791 2.628 -2.226 1.00 98.72 5 A 1 ATOM 37 C CB . LEU A 1 5 ? 4.132 4.669 -3.243 1.00 98.60 5 A 1 ATOM 38 C CG . LEU A 1 5 ? 4.500 6.149 -3.348 1.00 95.62 5 A 1 ATOM 39 C CD1 . LEU A 1 5 ? 5.267 6.404 -4.631 1.00 93.44 5 A 1 ATOM 40 C CD2 . LEU A 1 5 ? 3.238 7.005 -3.313 1.00 94.02 5 A 1 ATOM 41 N N . ILE A 1 6 ? 3.862 1.865 -1.831 1.00 98.81 6 A 1 ATOM 42 C CA . ILE A 1 6 ? 3.475 0.460 -1.903 1.00 98.82 6 A 1 ATOM 43 C C . ILE A 1 6 ? 2.494 0.119 -0.790 1.00 98.85 6 A 1 ATOM 44 O O . ILE A 1 6 ? 1.507 -0.582 -1.010 1.00 98.81 6 A 1 ATOM 45 C CB . ILE A 1 6 ? 4.711 -0.457 -1.818 1.00 98.75 6 A 1 ATOM 46 C CG1 . ILE A 1 6 ? 5.566 -0.291 -3.078 1.00 98.08 6 A 1 ATOM 47 C CG2 . ILE A 1 6 ? 4.287 -1.912 -1.659 1.00 97.81 6 A 1 ATOM 48 C CD1 . ILE A 1 6 ? 6.879 -1.036 -3.028 1.00 95.49 6 A 1 ATOM 49 N N . ILE A 1 7 ? 2.757 0.623 0.401 1.00 98.81 7 A 1 ATOM 50 C CA . ILE A 1 7 ? 1.889 0.366 1.545 1.00 98.80 7 A 1 ATOM 51 C C . ILE A 1 7 ? 0.500 0.945 1.294 1.00 98.82 7 A 1 ATOM 52 O O . ILE A 1 7 ? -0.513 0.274 1.503 1.00 98.78 7 A 1 ATOM 53 C CB . ILE A 1 7 ? 2.489 0.958 2.837 1.00 98.76 7 A 1 ATOM 54 C CG1 . ILE A 1 7 ? 3.765 0.199 3.216 1.00 98.17 7 A 1 ATOM 55 C CG2 . ILE A 1 7 ? 1.474 0.881 3.977 1.00 97.92 7 A 1 ATOM 56 C CD1 . ILE A 1 7 ? 4.541 0.829 4.354 1.00 96.25 7 A 1 ATOM 57 N N . LEU A 1 8 ? 0.441 2.181 0.838 1.00 98.78 8 A 1 ATOM 58 C CA . LEU A 1 8 ? -0.831 2.832 0.545 1.00 98.73 8 A 1 ATOM 59 C C . LEU A 1 8 ? -1.585 2.091 -0.554 1.00 98.78 8 A 1 ATOM 60 O O . LEU A 1 8 ? -2.802 1.926 -0.486 1.00 98.71 8 A 1 ATOM 61 C CB . LEU A 1 8 ? -0.598 4.286 0.123 1.00 98.60 8 A 1 ATOM 62 C CG . LEU A 1 8 ? -0.755 5.321 1.240 1.00 95.24 8 A 1 ATOM 63 C CD1 . LEU A 1 8 ? 0.080 4.944 2.456 1.00 93.71 8 A 1 ATOM 64 C CD2 . LEU A 1 8 ? -0.361 6.699 0.735 1.00 94.38 8 A 1 ATOM 65 N N . LEU A 1 9 ? -0.862 1.649 -1.572 1.00 98.55 9 A 1 ATOM 66 C CA . LEU A 1 9 ? -1.459 0.920 -2.683 1.00 98.50 9 A 1 ATOM 67 C C . LEU A 1 9 ? -2.051 -0.400 -2.208 1.00 98.66 9 A 1 ATOM 68 O O . LEU A 1 9 ? -3.177 -0.748 -2.565 1.00 98.57 9 A 1 ATOM 69 C CB . LEU A 1 9 ? -0.406 0.653 -3.761 1.00 98.29 9 A 1 ATOM 70 C CG . LEU A 1 9 ? -0.898 -0.145 -4.969 1.00 94.26 9 A 1 ATOM 71 C CD1 . LEU A 1 9 ? -2.023 0.599 -5.671 1.00 92.09 9 A 1 ATOM 72 C CD2 . LEU A 1 9 ? 0.253 -0.396 -5.929 1.00 92.76 9 A 1 ATOM 73 N N . ALA A 1 10 ? -1.289 -1.140 -1.406 1.00 98.76 10 A 1 ATOM 74 C CA . ALA A 1 10 ? -1.741 -2.426 -0.896 1.00 98.78 10 A 1 ATOM 75 C C . ALA A 1 10 ? -3.005 -2.271 -0.057 1.00 98.82 10 A 1 ATOM 76 O O . ALA A 1 10 ? -3.945 -3.058 -0.179 1.00 98.64 10 A 1 ATOM 77 C CB . ALA A 1 10 ? -0.635 -3.075 -0.067 1.00 98.61 10 A 1 ATOM 78 N N . ILE A 1 11 ? -3.036 -1.261 0.786 1.00 98.80 11 A 1 ATOM 79 C CA . ILE A 1 11 ? -4.189 -1.007 1.637 1.00 98.74 11 A 1 ATOM 80 C C . ILE A 1 11 ? -5.405 -0.651 0.788 1.00 98.76 11 A 1 ATOM 81 O O . ILE A 1 11 ? -6.513 -1.129 1.043 1.00 98.55 11 A 1 ATOM 82 C CB . ILE A 1 11 ? -3.894 0.125 2.639 1.00 98.58 11 A 1 ATOM 83 C CG1 . ILE A 1 11 ? -2.821 -0.324 3.638 1.00 97.58 11 A 1 ATOM 84 C CG2 . ILE A 1 11 ? -5.170 0.523 3.381 1.00 97.40 11 A 1 ATOM 85 C CD1 . ILE A 1 11 ? -2.332 0.780 4.549 1.00 96.02 11 A 1 ATOM 86 N N . SER A 1 12 ? -5.203 0.168 -0.222 1.00 98.83 12 A 1 ATOM 87 C CA . SER A 1 12 ? -6.288 0.586 -1.107 1.00 98.81 12 A 1 ATOM 88 C C . SER A 1 12 ? -6.890 -0.603 -1.851 1.00 98.83 12 A 1 ATOM 89 O O . SER A 1 12 ? -8.105 -0.698 -2.008 1.00 98.52 12 A 1 ATOM 90 C CB . SER A 1 12 ? -5.783 1.619 -2.108 1.00 98.56 12 A 1 ATOM 91 O OG . SER A 1 12 ? -5.353 2.790 -1.440 1.00 93.81 12 A 1 ATOM 92 N N . ILE A 1 13 ? -6.043 -1.520 -2.306 1.00 98.81 13 A 1 ATOM 93 C CA . ILE A 1 13 ? -6.500 -2.702 -3.029 1.00 98.76 13 A 1 ATOM 94 C C . ILE A 1 13 ? -7.352 -3.586 -2.128 1.00 98.78 13 A 1 ATOM 95 O O . ILE A 1 13 ? -8.433 -4.031 -2.516 1.00 98.58 13 A 1 ATOM 96 C CB . ILE A 1 13 ? -5.309 -3.509 -3.575 1.00 98.60 13 A 1 ATOM 97 C CG1 . ILE A 1 13 ? -4.579 -2.693 -4.649 1.00 97.59 13 A 1 ATOM 98 C CG2 . ILE A 1 13 ? -5.786 -4.838 -4.158 1.00 97.53 13 A 1 ATOM 99 C CD1 . ILE A 1 13 ? -3.277 -3.310 -5.103 1.00 95.64 13 A 1 ATOM 100 N N . VAL A 1 14 ? -6.866 -3.854 -0.924 1.00 98.83 14 A 1 ATOM 101 C CA . VAL A 1 14 ? -7.591 -4.695 0.025 1.00 98.77 14 A 1 ATOM 102 C C . VAL A 1 14 ? -8.895 -4.035 0.462 1.00 98.77 14 A 1 ATOM 103 O O . VAL A 1 14 ? -9.932 -4.694 0.570 1.00 98.39 14 A 1 ATOM 104 C CB . VAL A 1 14 ? -6.727 -4.997 1.259 1.00 98.44 14 A 1 ATOM 105 C CG1 . VAL A 1 14 ? -7.522 -5.793 2.282 1.00 96.99 14 A 1 ATOM 106 C CG2 . VAL A 1 14 ? -5.482 -5.760 0.851 1.00 97.44 14 A 1 ATOM 107 N N . ALA A 1 15 ? -8.849 -2.745 0.718 1.00 98.74 15 A 1 ATOM 108 C CA . ALA A 1 15 ? -10.019 -2.004 1.174 1.00 98.66 15 A 1 ATOM 109 C C . ALA A 1 15 ? -11.100 -1.898 0.101 1.00 98.69 15 A 1 ATOM 110 O O . ALA A 1 15 ? -12.284 -1.783 0.420 1.00 98.25 15 A 1 ATOM 111 C CB . ALA A 1 15 ? -9.603 -0.606 1.632 1.00 98.24 15 A 1 ATOM 112 N N . SER A 1 16 ? -10.712 -1.942 -1.164 1.00 98.61 16 A 1 ATOM 113 C CA . SER A 1 16 ? -11.659 -1.828 -2.273 1.00 98.46 16 A 1 ATOM 114 C C . SER A 1 16 ? -12.191 -3.184 -2.735 1.00 98.37 16 A 1 ATOM 115 O O . SER A 1 16 ? -12.910 -3.272 -3.729 1.00 96.74 16 A 1 ATOM 116 C CB . SER A 1 16 ? -11.006 -1.105 -3.453 1.00 97.74 16 A 1 ATOM 117 O OG . SER A 1 16 ? -9.932 -1.852 -3.973 1.00 91.66 16 A 1 ATOM 118 N N . ALA A 1 17 ? -11.842 -4.248 -2.019 1.00 97.93 17 A 1 ATOM 119 C CA . ALA A 1 17 ? -12.277 -5.584 -2.385 1.00 96.86 17 A 1 ATOM 120 C C . ALA A 1 17 ? -13.429 -6.058 -1.495 1.00 96.14 17 A 1 ATOM 121 O O . ALA A 1 17 ? -13.771 -5.355 -0.521 1.00 93.63 17 A 1 ATOM 122 C CB . ALA A 1 17 ? -11.097 -6.556 -2.307 1.00 95.14 17 A 1 ATOM 123 O OXT . ALA A 1 17 ? -13.995 -7.129 -1.769 1.00 88.67 17 A 1 #