# 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_spkb26334 # _entry.id spkb26334 # 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 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" "C3 H7 N O3" 105.093 SER y SERINE C([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 PHE 1 1 n LEU 2 1 n VAL 3 1 n LEU 4 1 n LEU 5 1 n LEU 6 1 n VAL 7 1 n SER 8 1 n LEU 9 1 n MET 10 1 n CYS 11 1 n TYR 12 1 n ALA 13 # _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 @ 2025-07-12 13:21:38)" _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 96.73 _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 PHE 1 2 96.41 1 1 A LEU 2 2 96.94 1 2 A VAL 3 2 98.21 1 3 A LEU 4 2 97.58 1 4 A LEU 5 2 97.66 1 5 A LEU 6 2 97.14 1 6 A VAL 7 2 98.23 1 7 A SER 8 2 97.55 1 8 A LEU 9 2 97.48 1 9 A MET 10 2 95.71 1 10 A CYS 11 2 97.54 1 11 A TYR 12 2 94.79 1 12 A ALA 13 2 93.28 1 13 # _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 PHE . 1 A 1 A 2 1 n LEU . 2 A 2 A 3 1 n VAL . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n VAL . 7 A 7 A 8 1 n SER . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n MET . 10 A 10 A 11 1 n CYS . 11 A 11 A 12 1 n TYR . 12 A 12 A 13 1 n ALA . 13 A 13 # _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 . PHE A 1 1 ? -6.087 6.347 -6.595 1.00 97.02 1 A 1 ATOM 2 C CA . PHE A 1 1 ? -5.974 4.932 -6.192 1.00 97.66 1 A 1 ATOM 3 C C . PHE A 1 1 ? -4.873 4.764 -5.147 1.00 98.22 1 A 1 ATOM 4 O O . PHE A 1 1 ? -3.723 4.529 -5.489 1.00 97.90 1 A 1 ATOM 5 C CB . PHE A 1 1 ? -5.654 4.106 -7.437 1.00 96.92 1 A 1 ATOM 6 C CG . PHE A 1 1 ? -6.189 2.704 -7.353 1.00 96.19 1 A 1 ATOM 7 C CD1 . PHE A 1 1 ? -7.348 2.424 -6.664 1.00 95.63 1 A 1 ATOM 8 C CD2 . PHE A 1 1 ? -5.529 1.675 -8.006 1.00 95.26 1 A 1 ATOM 9 C CE1 . PHE A 1 1 ? -7.854 1.136 -6.614 1.00 95.27 1 A 1 ATOM 10 C CE2 . PHE A 1 1 ? -6.032 0.384 -7.964 1.00 94.63 1 A 1 ATOM 11 C CZ . PHE A 1 1 ? -7.188 0.119 -7.268 1.00 95.78 1 A 1 ATOM 12 N N . LEU A 1 2 ? -5.227 4.917 -3.893 1.00 98.05 2 A 1 ATOM 13 C CA . LEU A 1 2 ? -4.261 4.826 -2.796 1.00 98.28 2 A 1 ATOM 14 C C . LEU A 1 2 ? -4.473 3.571 -1.961 1.00 98.57 2 A 1 ATOM 15 O O . LEU A 1 2 ? -3.534 3.056 -1.366 1.00 98.37 2 A 1 ATOM 16 C CB . LEU A 1 2 ? -4.398 6.057 -1.906 1.00 97.94 2 A 1 ATOM 17 C CG . LEU A 1 2 ? -5.826 6.246 -1.401 1.00 95.58 2 A 1 ATOM 18 C CD1 . LEU A 1 2 ? -5.802 7.022 -0.099 1.00 94.29 2 A 1 ATOM 19 C CD2 . LEU A 1 2 ? -6.668 6.979 -2.430 1.00 94.40 2 A 1 ATOM 20 N N . VAL A 1 3 ? -5.712 3.101 -1.907 1.00 98.68 3 A 1 ATOM 21 C CA . VAL A 1 3 ? -6.034 1.917 -1.105 1.00 98.71 3 A 1 ATOM 22 C C . VAL A 1 3 ? -5.226 0.712 -1.569 1.00 98.78 3 A 1 ATOM 23 O O . VAL A 1 3 ? -4.686 -0.040 -0.760 1.00 98.61 3 A 1 ATOM 24 C CB . VAL A 1 3 ? -7.545 1.615 -1.191 1.00 98.48 3 A 1 ATOM 25 C CG1 . VAL A 1 3 ? -7.951 1.314 -2.624 1.00 97.12 3 A 1 ATOM 26 C CG2 . VAL A 1 3 ? -7.889 0.446 -0.292 1.00 97.06 3 A 1 ATOM 27 N N . LEU A 1 4 ? -5.150 0.534 -2.854 1.00 98.62 4 A 1 ATOM 28 C CA . LEU A 1 4 ? -4.398 -0.595 -3.411 1.00 98.65 4 A 1 ATOM 29 C C . LEU A 1 4 ? -2.917 -0.462 -3.086 1.00 98.73 4 A 1 ATOM 30 O O . LEU A 1 4 ? -2.269 -1.425 -2.682 1.00 98.59 4 A 1 ATOM 31 C CB . LEU A 1 4 ? -4.599 -0.643 -4.924 1.00 98.48 4 A 1 ATOM 32 C CG . LEU A 1 4 ? -3.865 -1.812 -5.572 1.00 96.34 4 A 1 ATOM 33 C CD1 . LEU A 1 4 ? -4.503 -3.132 -5.158 1.00 95.42 4 A 1 ATOM 34 C CD2 . LEU A 1 4 ? -3.886 -1.680 -7.084 1.00 95.78 4 A 1 ATOM 35 N N . LEU A 1 5 ? -2.407 0.726 -3.241 1.00 98.54 5 A 1 ATOM 36 C CA . LEU A 1 5 ? -0.998 0.991 -2.963 1.00 98.53 5 A 1 ATOM 37 C C . LEU A 1 5 ? -0.711 0.824 -1.478 1.00 98.65 5 A 1 ATOM 38 O O . LEU A 1 5 ? 0.355 0.357 -1.094 1.00 98.53 5 A 1 ATOM 39 C CB . LEU A 1 5 ? -0.675 2.414 -3.402 1.00 98.38 5 A 1 ATOM 40 C CG . LEU A 1 5 ? -1.127 2.687 -4.827 1.00 97.11 5 A 1 ATOM 41 C CD1 . LEU A 1 5 ? -0.861 4.143 -5.181 1.00 95.55 5 A 1 ATOM 42 C CD2 . LEU A 1 5 ? -0.389 1.772 -5.797 1.00 96.00 5 A 1 ATOM 43 N N . LEU A 1 6 ? -1.658 1.204 -0.663 1.00 98.55 6 A 1 ATOM 44 C CA . LEU A 1 6 ? -1.508 1.093 0.790 1.00 98.55 6 A 1 ATOM 45 C C . LEU A 1 6 ? -1.374 -0.370 1.197 1.00 98.65 6 A 1 ATOM 46 O O . LEU A 1 6 ? -0.537 -0.725 2.020 1.00 98.55 6 A 1 ATOM 47 C CB . LEU A 1 6 ? -2.734 1.705 1.464 1.00 98.34 6 A 1 ATOM 48 C CG . LEU A 1 6 ? -2.572 1.809 2.974 1.00 95.28 6 A 1 ATOM 49 C CD1 . LEU A 1 6 ? -1.733 3.029 3.322 1.00 94.22 6 A 1 ATOM 50 C CD2 . LEU A 1 6 ? -3.926 1.902 3.649 1.00 94.99 6 A 1 ATOM 51 N N . VAL A 1 7 ? -2.203 -1.207 0.636 1.00 98.69 7 A 1 ATOM 52 C CA . VAL A 1 7 ? -2.175 -2.639 0.947 1.00 98.62 7 A 1 ATOM 53 C C . VAL A 1 7 ? -0.828 -3.229 0.558 1.00 98.70 7 A 1 ATOM 54 O O . VAL A 1 7 ? -0.257 -4.045 1.278 1.00 98.56 7 A 1 ATOM 55 C CB . VAL A 1 7 ? -3.298 -3.367 0.197 1.00 98.36 7 A 1 ATOM 56 C CG1 . VAL A 1 7 ? -3.168 -4.870 0.378 1.00 97.26 7 A 1 ATOM 57 C CG2 . VAL A 1 7 ? -4.644 -2.900 0.719 1.00 97.42 7 A 1 ATOM 58 N N . SER A 1 8 ? -0.346 -2.820 -0.558 1.00 98.48 8 A 1 ATOM 59 C CA . SER A 1 8 ? 0.939 -3.311 -1.046 1.00 98.46 8 A 1 ATOM 60 C C . SER A 1 8 ? 2.048 -2.922 -0.077 1.00 98.53 8 A 1 ATOM 61 O O . SER A 1 8 ? 2.981 -3.682 0.147 1.00 98.15 8 A 1 ATOM 62 C CB . SER A 1 8 ? 1.219 -2.721 -2.417 1.00 98.09 8 A 1 ATOM 63 O OG . SER A 1 8 ? 2.334 -3.372 -2.967 1.00 93.60 8 A 1 ATOM 64 N N . LEU A 1 9 ? 1.926 -1.762 0.496 1.00 98.65 9 A 1 ATOM 65 C CA . LEU A 1 9 ? 2.924 -1.273 1.446 1.00 98.53 9 A 1 ATOM 66 C C . LEU A 1 9 ? 2.948 -2.144 2.695 1.00 98.57 9 A 1 ATOM 67 O O . LEU A 1 9 ? 4.008 -2.436 3.238 1.00 98.22 9 A 1 ATOM 68 C CB . LEU A 1 9 ? 2.586 0.162 1.829 1.00 98.25 9 A 1 ATOM 69 C CG . LEU A 1 9 ? 3.715 0.815 2.608 1.00 96.78 9 A 1 ATOM 70 C CD1 . LEU A 1 9 ? 4.707 1.448 1.649 1.00 95.52 9 A 1 ATOM 71 C CD2 . LEU A 1 9 ? 3.163 1.865 3.555 1.00 95.36 9 A 1 ATOM 72 N N . MET A 1 10 ? 1.788 -2.557 3.152 1.00 98.56 10 A 1 ATOM 73 C CA . MET A 1 10 ? 1.677 -3.385 4.355 1.00 98.38 10 A 1 ATOM 74 C C . MET A 1 10 ? 2.424 -4.703 4.159 1.00 98.43 10 A 1 ATOM 75 O O . MET A 1 10 ? 3.127 -5.170 5.044 1.00 97.78 10 A 1 ATOM 76 C CB . MET A 1 10 ? 0.204 -3.648 4.649 1.00 97.93 10 A 1 ATOM 77 C CG . MET A 1 10 ? 0.017 -4.101 6.073 1.00 96.31 10 A 1 ATOM 78 S SD . MET A 1 10 ? -1.693 -4.069 6.557 1.00 92.31 10 A 1 ATOM 79 C CE . MET A 1 10 ? -1.568 -4.878 8.138 1.00 86.00 10 A 1 ATOM 80 N N . CYS A 1 11 ? 2.269 -5.285 3.010 1.00 98.35 11 A 1 ATOM 81 C CA . CYS A 1 11 ? 2.949 -6.543 2.691 1.00 98.33 11 A 1 ATOM 82 C C . CYS A 1 11 ? 4.402 -6.279 2.312 1.00 98.39 11 A 1 ATOM 83 O O . CYS A 1 11 ? 5.236 -7.175 2.320 1.00 97.85 11 A 1 ATOM 84 C CB . CYS A 1 11 ? 2.231 -7.226 1.532 1.00 97.75 11 A 1 ATOM 85 S SG . CYS A 1 11 ? 2.681 -8.966 1.434 1.00 94.58 11 A 1 ATOM 86 N N . TYR A 1 12 ? 4.657 -5.044 1.988 1.00 98.22 12 A 1 ATOM 87 C CA . TYR A 1 12 ? 6.007 -4.642 1.591 1.00 98.02 12 A 1 ATOM 88 C C . TYR A 1 12 ? 6.995 -4.872 2.727 1.00 97.98 12 A 1 ATOM 89 O O . TYR A 1 12 ? 8.149 -5.237 2.508 1.00 97.00 12 A 1 ATOM 90 C CB . TYR A 1 12 ? 5.976 -3.167 1.199 1.00 97.35 12 A 1 ATOM 91 C CG . TYR A 1 12 ? 7.309 -2.685 0.696 1.00 95.18 12 A 1 ATOM 92 C CD1 . TYR A 1 12 ? 8.292 -2.276 1.582 1.00 93.32 12 A 1 ATOM 93 C CD2 . TYR A 1 12 ? 7.575 -2.639 -0.665 1.00 92.54 12 A 1 ATOM 94 C CE1 . TYR A 1 12 ? 9.525 -1.835 1.122 1.00 92.56 12 A 1 ATOM 95 C CE2 . TYR A 1 12 ? 8.810 -2.196 -1.133 1.00 91.80 12 A 1 ATOM 96 C CZ . TYR A 1 12 ? 9.774 -1.797 -0.230 1.00 92.47 12 A 1 ATOM 97 O OH . TYR A 1 12 ? 10.991 -1.362 -0.687 1.00 91.05 12 A 1 ATOM 98 N N . ALA A 1 13 ? 6.538 -4.658 3.945 1.00 97.09 13 A 1 ATOM 99 C CA . ALA A 1 13 ? 7.401 -4.834 5.107 1.00 95.60 13 A 1 ATOM 100 C C . ALA A 1 13 ? 6.583 -4.992 6.390 1.00 94.40 13 A 1 ATOM 101 O O . ALA A 1 13 ? 5.402 -4.630 6.395 1.00 92.17 13 A 1 ATOM 102 C CB . ALA A 1 13 ? 8.323 -3.630 5.237 1.00 94.01 13 A 1 ATOM 103 O OXT . ALA A 1 13 ? 7.124 -5.456 7.397 1.00 86.43 13 A 1 #