# 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_spkb09086 # _entry.id spkb09086 # 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" "C3 H7 N O2 S" 121.158 CYS y CYSTEINE C([C@@H](C(=O)O)N)S ? "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" "C9 H11 N O2" 165.189 PHE y PHENYLALANINE c1ccc(cc1)C[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" "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 MET 2 1 n HIS 3 1 n LEU 4 1 n ALA 5 1 n PHE 6 1 n LEU 7 1 n VAL 8 1 n LEU 9 1 n LEU 10 1 n CYS 11 1 n LEU 12 1 n PRO 13 1 n VAL 14 1 n CYS 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 @ 2025-07-08 23:36:35)" _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 90.77 _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 82.03 1 1 A MET 2 2 85.93 1 2 A HIS 3 2 85.09 1 3 A LEU 4 2 90.33 1 4 A ALA 5 2 95.19 1 5 A PHE 6 2 91.89 1 6 A LEU 7 2 93.07 1 7 A VAL 8 2 94.65 1 8 A LEU 9 2 93.08 1 9 A LEU 10 2 93.86 1 10 A CYS 11 2 93.94 1 11 A LEU 12 2 92.92 1 12 A PRO 13 2 94.60 1 13 A VAL 14 2 92.26 1 14 A CYS 15 2 92.68 1 15 A SER 16 2 90.06 1 16 A ALA 17 2 85.03 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 MET . 2 A 2 A 3 1 n HIS . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n PHE . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n VAL . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n CYS . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n PRO . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n CYS . 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 ? -5.165 10.787 3.061 1.00 87.62 1 A 1 ATOM 2 C CA . MET A 1 1 ? -5.786 9.468 2.832 1.00 89.31 1 A 1 ATOM 3 C C . MET A 1 1 ? -4.813 8.348 3.207 1.00 90.21 1 A 1 ATOM 4 O O . MET A 1 1 ? -4.202 7.732 2.339 1.00 88.58 1 A 1 ATOM 5 C CB . MET A 1 1 ? -6.182 9.315 1.362 1.00 84.73 1 A 1 ATOM 6 C CG . MET A 1 1 ? -7.136 10.398 0.899 1.00 78.28 1 A 1 ATOM 7 S SD . MET A 1 1 ? -7.508 10.235 -0.853 1.00 73.84 1 A 1 ATOM 8 C CE . MET A 1 1 ? -8.398 11.751 -1.131 1.00 63.68 1 A 1 ATOM 9 N N . MET A 1 2 ? -4.681 8.107 4.504 1.00 92.02 2 A 1 ATOM 10 C CA . MET A 1 2 ? -3.743 7.092 4.995 1.00 92.81 2 A 1 ATOM 11 C C . MET A 1 2 ? -4.202 5.674 4.649 1.00 93.67 2 A 1 ATOM 12 O O . MET A 1 2 ? -3.386 4.763 4.545 1.00 91.66 2 A 1 ATOM 13 C CB . MET A 1 2 ? -3.566 7.237 6.509 1.00 90.09 2 A 1 ATOM 14 C CG . MET A 1 2 ? -4.840 7.006 7.303 1.00 83.23 2 A 1 ATOM 15 S SD . MET A 1 2 ? -4.590 7.319 9.055 1.00 77.50 2 A 1 ATOM 16 C CE . MET A 1 2 ? -6.188 6.855 9.695 1.00 66.43 2 A 1 ATOM 17 N N . HIS A 1 3 ? -5.503 5.503 4.453 1.00 91.20 3 A 1 ATOM 18 C CA . HIS A 1 3 ? -6.059 4.198 4.105 1.00 92.79 3 A 1 ATOM 19 C C . HIS A 1 3 ? -5.574 3.753 2.731 1.00 94.05 3 A 1 ATOM 20 O O . HIS A 1 3 ? -5.248 2.586 2.519 1.00 93.05 3 A 1 ATOM 21 C CB . HIS A 1 3 ? -7.587 4.256 4.141 1.00 91.37 3 A 1 ATOM 22 C CG . HIS A 1 3 ? -8.213 2.908 4.343 1.00 84.84 3 A 1 ATOM 23 N ND1 . HIS A 1 3 ? -8.243 2.256 5.551 1.00 75.17 3 A 1 ATOM 24 C CD2 . HIS A 1 3 ? -8.845 2.104 3.455 1.00 74.40 3 A 1 ATOM 25 C CE1 . HIS A 1 3 ? -8.868 1.096 5.387 1.00 76.63 3 A 1 ATOM 26 N NE2 . HIS A 1 3 ? -9.245 0.972 4.124 1.00 77.39 3 A 1 ATOM 27 N N . LEU A 1 4 ? -5.511 4.689 1.804 1.00 93.88 4 A 1 ATOM 28 C CA . LEU A 1 4 ? -5.018 4.405 0.459 1.00 94.44 4 A 1 ATOM 29 C C . LEU A 1 4 ? -3.538 4.053 0.495 1.00 95.24 4 A 1 ATOM 30 O O . LEU A 1 4 ? -3.082 3.167 -0.229 1.00 94.62 4 A 1 ATOM 31 C CB . LEU A 1 4 ? -5.259 5.616 -0.448 1.00 93.65 4 A 1 ATOM 32 C CG . LEU A 1 4 ? -6.385 5.411 -1.458 1.00 86.21 4 A 1 ATOM 33 C CD1 . LEU A 1 4 ? -6.825 6.738 -2.051 1.00 82.47 4 A 1 ATOM 34 C CD2 . LEU A 1 4 ? -5.934 4.461 -2.554 1.00 82.13 4 A 1 ATOM 35 N N . ALA A 1 5 ? -2.812 4.741 1.344 1.00 94.85 5 A 1 ATOM 36 C CA . ALA A 1 5 ? -1.382 4.493 1.493 1.00 95.28 5 A 1 ATOM 37 C C . ALA A 1 5 ? -1.125 3.065 1.973 1.00 95.94 5 A 1 ATOM 38 O O . ALA A 1 5 ? -0.150 2.433 1.572 1.00 95.31 5 A 1 ATOM 39 C CB . ALA A 1 5 ? -0.783 5.499 2.470 1.00 94.55 5 A 1 ATOM 40 N N . PHE A 1 6 ? -2.008 2.573 2.814 1.00 94.63 6 A 1 ATOM 41 C CA . PHE A 1 6 ? -1.902 1.210 3.327 1.00 94.86 6 A 1 ATOM 42 C C . PHE A 1 6 ? -2.049 0.194 2.200 1.00 95.69 6 A 1 ATOM 43 O O . PHE A 1 6 ? -1.306 -0.786 2.134 1.00 95.23 6 A 1 ATOM 44 C CB . PHE A 1 6 ? -2.969 0.977 4.398 1.00 94.67 6 A 1 ATOM 45 C CG . PHE A 1 6 ? -2.918 -0.409 4.992 1.00 92.86 6 A 1 ATOM 46 C CD1 . PHE A 1 6 ? -1.885 -0.768 5.846 1.00 89.40 6 A 1 ATOM 47 C CD2 . PHE A 1 6 ? -3.901 -1.337 4.698 1.00 89.21 6 A 1 ATOM 48 C CE1 . PHE A 1 6 ? -1.830 -2.043 6.396 1.00 88.17 6 A 1 ATOM 49 C CE2 . PHE A 1 6 ? -3.849 -2.617 5.243 1.00 87.57 6 A 1 ATOM 50 C CZ . PHE A 1 6 ? -2.814 -2.969 6.092 1.00 88.52 6 A 1 ATOM 51 N N . LEU A 1 7 ? -2.998 0.440 1.306 1.00 94.95 7 A 1 ATOM 52 C CA . LEU A 1 7 ? -3.227 -0.446 0.168 1.00 95.17 7 A 1 ATOM 53 C C . LEU A 1 7 ? -2.024 -0.447 -0.765 1.00 95.83 7 A 1 ATOM 54 O O . LEU A 1 7 ? -1.625 -1.493 -1.282 1.00 95.64 7 A 1 ATOM 55 C CB . LEU A 1 7 ? -4.481 -0.011 -0.596 1.00 95.29 7 A 1 ATOM 56 C CG . LEU A 1 7 ? -5.788 -0.159 0.177 1.00 91.52 7 A 1 ATOM 57 C CD1 . LEU A 1 7 ? -6.940 0.441 -0.614 1.00 88.03 7 A 1 ATOM 58 C CD2 . LEU A 1 7 ? -6.075 -1.627 0.478 1.00 88.12 7 A 1 ATOM 59 N N . VAL A 1 8 ? -1.466 0.718 -0.966 1.00 95.57 8 A 1 ATOM 60 C CA . VAL A 1 8 ? -0.282 0.860 -1.814 1.00 95.69 8 A 1 ATOM 61 C C . VAL A 1 8 ? 0.899 0.130 -1.186 1.00 96.01 8 A 1 ATOM 62 O O . VAL A 1 8 ? 1.689 -0.518 -1.877 1.00 95.51 8 A 1 ATOM 63 C CB . VAL A 1 8 ? 0.066 2.345 -2.035 1.00 95.33 8 A 1 ATOM 64 C CG1 . VAL A 1 8 ? 1.362 2.493 -2.828 1.00 92.23 8 A 1 ATOM 65 C CG2 . VAL A 1 8 ? -1.067 3.054 -2.762 1.00 92.20 8 A 1 ATOM 66 N N . LEU A 1 9 ? 0.999 0.232 0.125 1.00 95.01 9 A 1 ATOM 67 C CA . LEU A 1 9 ? 2.074 -0.422 0.866 1.00 94.98 9 A 1 ATOM 68 C C . LEU A 1 9 ? 1.984 -1.941 0.722 1.00 95.60 9 A 1 ATOM 69 O O . LEU A 1 9 ? 3.008 -2.620 0.622 1.00 95.25 9 A 1 ATOM 70 C CB . LEU A 1 9 ? 2.002 -0.023 2.342 1.00 95.10 9 A 1 ATOM 71 C CG . LEU A 1 9 ? 3.191 -0.472 3.188 1.00 90.88 9 A 1 ATOM 72 C CD1 . LEU A 1 9 ? 4.461 0.271 2.775 1.00 88.68 9 A 1 ATOM 73 C CD2 . LEU A 1 9 ? 2.907 -0.244 4.663 1.00 89.10 9 A 1 ATOM 74 N N . LEU A 1 10 ? 0.768 -2.462 0.695 1.00 96.02 10 A 1 ATOM 75 C CA . LEU A 1 10 ? 0.545 -3.894 0.524 1.00 95.66 10 A 1 ATOM 76 C C . LEU A 1 10 ? 0.874 -4.333 -0.895 1.00 96.16 10 A 1 ATOM 77 O O . LEU A 1 10 ? 1.370 -5.444 -1.113 1.00 95.45 10 A 1 ATOM 78 C CB . LEU A 1 10 ? -0.913 -4.232 0.854 1.00 95.28 10 A 1 ATOM 79 C CG . LEU A 1 10 ? -1.234 -4.317 2.344 1.00 92.01 10 A 1 ATOM 80 C CD1 . LEU A 1 10 ? -2.745 -4.406 2.548 1.00 90.08 10 A 1 ATOM 81 C CD2 . LEU A 1 10 ? -0.553 -5.518 2.980 1.00 90.20 10 A 1 ATOM 82 N N . CYS A 1 11 ? 0.606 -3.465 -1.838 1.00 95.35 11 A 1 ATOM 83 C CA . CYS A 1 11 ? 0.866 -3.762 -3.241 1.00 95.46 11 A 1 ATOM 84 C C . CYS A 1 11 ? 2.360 -3.773 -3.537 1.00 95.61 11 A 1 ATOM 85 O O . CYS A 1 11 ? 2.815 -4.485 -4.430 1.00 93.40 11 A 1 ATOM 86 C CB . CYS A 1 11 ? 0.163 -2.737 -4.132 1.00 94.16 11 A 1 ATOM 87 S SG . CYS A 1 11 ? 0.264 -3.115 -5.895 1.00 89.66 11 A 1 ATOM 88 N N . LEU A 1 12 ? 3.103 -2.992 -2.778 1.00 95.63 12 A 1 ATOM 89 C CA . LEU A 1 12 ? 4.548 -2.884 -2.979 1.00 95.09 12 A 1 ATOM 90 C C . LEU A 1 12 ? 5.236 -4.255 -2.986 1.00 95.41 12 A 1 ATOM 91 O O . LEU A 1 12 ? 5.900 -4.602 -3.969 1.00 94.15 12 A 1 ATOM 92 C CB . LEU A 1 12 ? 5.156 -1.961 -1.918 1.00 94.50 12 A 1 ATOM 93 C CG . LEU A 1 12 ? 6.591 -1.532 -2.198 1.00 91.23 12 A 1 ATOM 94 C CD1 . LEU A 1 12 ? 6.634 -0.449 -3.266 1.00 89.02 12 A 1 ATOM 95 C CD2 . LEU A 1 12 ? 7.250 -1.038 -0.917 1.00 88.33 12 A 1 ATOM 96 N N . PRO A 1 13 ? 5.094 -5.052 -1.918 1.00 95.64 13 A 1 ATOM 97 C CA . PRO A 1 13 ? 5.723 -6.376 -1.895 1.00 95.17 13 A 1 ATOM 98 C C . PRO A 1 13 ? 5.050 -7.366 -2.833 1.00 95.40 13 A 1 ATOM 99 O O . PRO A 1 13 ? 5.726 -8.209 -3.432 1.00 92.99 13 A 1 ATOM 100 C CB . PRO A 1 13 ? 5.575 -6.820 -0.434 1.00 94.01 13 A 1 ATOM 101 C CG . PRO A 1 13 ? 4.394 -6.067 0.073 1.00 93.31 13 A 1 ATOM 102 C CD . PRO A 1 13 ? 4.404 -4.748 -0.664 1.00 95.68 13 A 1 ATOM 103 N N . VAL A 1 14 ? 3.745 -7.278 -2.977 1.00 95.19 14 A 1 ATOM 104 C CA . VAL A 1 14 ? 2.989 -8.179 -3.844 1.00 94.70 14 A 1 ATOM 105 C C . VAL A 1 14 ? 3.311 -7.933 -5.312 1.00 94.69 14 A 1 ATOM 106 O O . VAL A 1 14 ? 3.526 -8.879 -6.078 1.00 92.16 14 A 1 ATOM 107 C CB . VAL A 1 14 ? 1.476 -8.034 -3.604 1.00 93.22 14 A 1 ATOM 108 C CG1 . VAL A 1 14 ? 0.690 -8.923 -4.560 1.00 87.61 14 A 1 ATOM 109 C CG2 . VAL A 1 14 ? 1.132 -8.388 -2.168 1.00 88.28 14 A 1 ATOM 110 N N . CYS A 1 15 ? 3.354 -6.667 -5.690 1.00 94.19 15 A 1 ATOM 111 C CA . CYS A 1 15 ? 3.642 -6.294 -7.068 1.00 94.15 15 A 1 ATOM 112 C C . CYS A 1 15 ? 5.107 -6.552 -7.418 1.00 94.12 15 A 1 ATOM 113 O O . CYS A 1 15 ? 5.445 -6.803 -8.569 1.00 91.52 15 A 1 ATOM 114 C CB . CYS A 1 15 ? 3.286 -4.819 -7.298 1.00 92.67 15 A 1 ATOM 115 S SG . CYS A 1 15 ? 1.497 -4.513 -7.297 1.00 89.44 15 A 1 ATOM 116 N N . SER A 1 16 ? 5.954 -6.474 -6.419 1.00 93.45 16 A 1 ATOM 117 C CA . SER A 1 16 ? 7.380 -6.707 -6.610 1.00 93.05 16 A 1 ATOM 118 C C . SER A 1 16 ? 7.690 -8.199 -6.692 1.00 92.37 16 A 1 ATOM 119 O O . SER A 1 16 ? 8.650 -8.607 -7.354 1.00 88.89 16 A 1 ATOM 120 C CB . SER A 1 16 ? 8.174 -6.072 -5.468 1.00 90.96 16 A 1 ATOM 121 O OG . SER A 1 16 ? 9.558 -6.132 -5.725 1.00 81.62 16 A 1 ATOM 122 N N . ALA A 1 17 ? 6.886 -9.010 -6.021 1.00 92.44 17 A 1 ATOM 123 C CA . ALA A 1 17 ? 7.060 -10.459 -5.988 1.00 89.83 17 A 1 ATOM 124 C C . ALA A 1 17 ? 6.595 -11.087 -7.295 1.00 86.59 17 A 1 ATOM 125 O O . ALA A 1 17 ? 7.321 -11.943 -7.836 1.00 80.60 17 A 1 ATOM 126 C CB . ALA A 1 17 ? 6.302 -11.055 -4.805 1.00 85.30 17 A 1 ATOM 127 O OXT . ALA A 1 17 ? 5.495 -10.749 -7.751 1.00 75.43 17 A 1 #