# 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_spkb32753 # _entry.id spkb32753 # 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" "C2 H5 N O2" 75.067 GLY y GLYCINE C(C(=O)O)N ? "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" "C3 H7 N O3" 105.093 SER y SERINE C([C@@H](C(=O)O)N)O ? "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 PHE 2 1 n VAL 3 1 n LEU 4 1 n LEU 5 1 n TYR 6 1 n VAL 7 1 n THR 8 1 n SER 9 1 n PHE 10 1 n ALA 11 1 n ILE 12 1 n CYS 13 1 n ALA 14 1 n SER 15 1 n GLY 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 @ 2025-07-12 10:15:05)" _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 95.98 _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 91.55 1 1 A PHE 2 2 94.84 1 2 A VAL 3 2 97.84 1 3 A LEU 4 2 96.38 1 4 A LEU 5 2 95.92 1 5 A TYR 6 2 96.38 1 6 A VAL 7 2 98.08 1 7 A THR 8 2 96.62 1 8 A SER 9 2 97.45 1 9 A PHE 10 2 96.30 1 10 A ALA 11 2 98.41 1 11 A ILE 12 2 97.22 1 12 A CYS 13 2 96.84 1 13 A ALA 14 2 97.94 1 14 A SER 15 2 95.10 1 15 A GLY 16 2 88.81 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 PHE . 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 TYR . 6 A 6 A 7 1 n VAL . 7 A 7 A 8 1 n THR . 8 A 8 A 9 1 n SER . 9 A 9 A 10 1 n PHE . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n ILE . 12 A 12 A 13 1 n CYS . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n SER . 15 A 15 A 16 1 n GLY . 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 ? -7.224 -1.560 10.503 1.00 96.24 1 A 1 ATOM 2 C CA . MET A 1 1 ? -6.270 -0.555 10.006 1.00 96.67 1 A 1 ATOM 3 C C . MET A 1 1 ? -5.652 -0.989 8.671 1.00 96.78 1 A 1 ATOM 4 O O . MET A 1 1 ? -4.441 -1.139 8.552 1.00 95.81 1 A 1 ATOM 5 C CB . MET A 1 1 ? -5.167 -0.346 11.046 1.00 93.72 1 A 1 ATOM 6 C CG . MET A 1 1 ? -5.335 0.936 11.826 1.00 87.62 1 A 1 ATOM 7 S SD . MET A 1 1 ? -4.019 1.150 13.023 1.00 86.35 1 A 1 ATOM 8 C CE . MET A 1 1 ? -4.237 2.889 13.413 1.00 79.23 1 A 1 ATOM 9 N N . PHE A 1 2 ? -6.501 -1.178 7.701 1.00 97.03 2 A 1 ATOM 10 C CA . PHE A 1 2 ? -6.045 -1.600 6.378 1.00 97.76 2 A 1 ATOM 11 C C . PHE A 1 2 ? -5.571 -0.409 5.547 1.00 98.34 2 A 1 ATOM 12 O O . PHE A 1 2 ? -4.671 -0.536 4.716 1.00 98.10 2 A 1 ATOM 13 C CB . PHE A 1 2 ? -7.183 -2.325 5.661 1.00 96.88 2 A 1 ATOM 14 C CG . PHE A 1 2 ? -7.366 -3.743 6.142 1.00 94.89 2 A 1 ATOM 15 C CD1 . PHE A 1 2 ? -6.415 -4.704 5.842 1.00 93.45 2 A 1 ATOM 16 C CD2 . PHE A 1 2 ? -8.481 -4.102 6.877 1.00 92.45 2 A 1 ATOM 17 C CE1 . PHE A 1 2 ? -6.569 -6.015 6.274 1.00 91.37 2 A 1 ATOM 18 C CE2 . PHE A 1 2 ? -8.645 -5.409 7.315 1.00 91.28 2 A 1 ATOM 19 C CZ . PHE A 1 2 ? -7.688 -6.367 7.014 1.00 91.66 2 A 1 ATOM 20 N N . VAL A 1 3 ? -6.176 0.746 5.777 1.00 98.49 3 A 1 ATOM 21 C CA . VAL A 1 3 ? -5.798 1.959 5.046 1.00 98.56 3 A 1 ATOM 22 C C . VAL A 1 3 ? -4.337 2.322 5.317 1.00 98.71 3 A 1 ATOM 23 O O . VAL A 1 3 ? -3.667 2.918 4.470 1.00 98.57 3 A 1 ATOM 24 C CB . VAL A 1 3 ? -6.727 3.133 5.437 1.00 98.26 3 A 1 ATOM 25 C CG1 . VAL A 1 3 ? -6.418 3.635 6.847 1.00 96.10 3 A 1 ATOM 26 C CG2 . VAL A 1 3 ? -6.601 4.271 4.432 1.00 96.17 3 A 1 ATOM 27 N N . LEU A 1 4 ? -3.849 1.962 6.492 1.00 98.41 4 A 1 ATOM 28 C CA . LEU A 1 4 ? -2.466 2.241 6.875 1.00 98.48 4 A 1 ATOM 29 C C . LEU A 1 4 ? -1.505 1.437 6.000 1.00 98.58 4 A 1 ATOM 30 O O . LEU A 1 4 ? -0.480 1.945 5.546 1.00 98.44 4 A 1 ATOM 31 C CB . LEU A 1 4 ? -2.251 1.902 8.359 1.00 98.30 4 A 1 ATOM 32 C CG . LEU A 1 4 ? -1.417 2.931 9.125 1.00 94.15 4 A 1 ATOM 33 C CD1 . LEU A 1 4 ? -0.017 3.060 8.533 1.00 92.21 4 A 1 ATOM 34 C CD2 . LEU A 1 4 ? -2.122 4.281 9.117 1.00 92.50 4 A 1 ATOM 35 N N . LEU A 1 5 ? -1.851 0.187 5.762 1.00 98.29 5 A 1 ATOM 36 C CA . LEU A 1 5 ? -1.037 -0.688 4.914 1.00 98.36 5 A 1 ATOM 37 C C . LEU A 1 5 ? -1.045 -0.197 3.470 1.00 98.53 5 A 1 ATOM 38 O O . LEU A 1 5 ? -0.055 -0.325 2.748 1.00 98.42 5 A 1 ATOM 39 C CB . LEU A 1 5 ? -1.588 -2.114 4.986 1.00 98.14 5 A 1 ATOM 40 C CG . LEU A 1 5 ? -0.843 -3.010 5.966 1.00 93.36 5 A 1 ATOM 41 C CD1 . LEU A 1 5 ? -1.720 -4.178 6.393 1.00 90.94 5 A 1 ATOM 42 C CD2 . LEU A 1 5 ? 0.437 -3.532 5.326 1.00 91.31 5 A 1 ATOM 43 N N . TYR A 1 6 ? -2.168 0.365 3.074 1.00 98.20 6 A 1 ATOM 44 C CA . TYR A 1 6 ? -2.321 0.886 1.715 1.00 98.31 6 A 1 ATOM 45 C C . TYR A 1 6 ? -1.456 2.128 1.502 1.00 98.44 6 A 1 ATOM 46 O O . TYR A 1 6 ? -0.777 2.259 0.485 1.00 98.28 6 A 1 ATOM 47 C CB . TYR A 1 6 ? -3.800 1.207 1.470 1.00 98.19 6 A 1 ATOM 48 C CG . TYR A 1 6 ? -4.041 1.929 0.161 1.00 97.14 6 A 1 ATOM 49 C CD1 . TYR A 1 6 ? -3.893 1.261 -1.051 1.00 95.30 6 A 1 ATOM 50 C CD2 . TYR A 1 6 ? -4.421 3.264 0.152 1.00 95.10 6 A 1 ATOM 51 C CE1 . TYR A 1 6 ? -4.118 1.921 -2.252 1.00 94.31 6 A 1 ATOM 52 C CE2 . TYR A 1 6 ? -4.644 3.930 -1.051 1.00 94.47 6 A 1 ATOM 53 C CZ . TYR A 1 6 ? -4.492 3.255 -2.246 1.00 95.12 6 A 1 ATOM 54 O OH . TYR A 1 6 ? -4.714 3.911 -3.431 1.00 93.75 6 A 1 ATOM 55 N N . VAL A 1 7 ? -1.495 3.032 2.458 1.00 98.53 7 A 1 ATOM 56 C CA . VAL A 1 7 ? -0.724 4.277 2.347 1.00 98.52 7 A 1 ATOM 57 C C . VAL A 1 7 ? 0.778 4.004 2.437 1.00 98.62 7 A 1 ATOM 58 O O . VAL A 1 7 ? 1.580 4.682 1.791 1.00 98.47 7 A 1 ATOM 59 C CB . VAL A 1 7 ? -1.154 5.286 3.435 1.00 98.31 7 A 1 ATOM 60 C CG1 . VAL A 1 7 ? -0.652 4.864 4.810 1.00 97.04 7 A 1 ATOM 61 C CG2 . VAL A 1 7 ? -0.639 6.682 3.104 1.00 97.07 7 A 1 ATOM 62 N N . THR A 1 8 ? 1.158 3.010 3.218 1.00 98.30 8 A 1 ATOM 63 C CA . THR A 1 8 ? 2.573 2.658 3.367 1.00 98.23 8 A 1 ATOM 64 C C . THR A 1 8 ? 3.115 2.043 2.084 1.00 98.36 8 A 1 ATOM 65 O O . THR A 1 8 ? 4.196 2.417 1.619 1.00 98.06 8 A 1 ATOM 66 C CB . THR A 1 8 ? 2.779 1.670 4.527 1.00 97.81 8 A 1 ATOM 67 O OG1 . THR A 1 8 ? 1.610 0.903 4.751 1.00 92.95 8 A 1 ATOM 68 C CG2 . THR A 1 8 ? 3.149 2.408 5.800 1.00 92.63 8 A 1 ATOM 69 N N . SER A 1 9 ? 2.366 1.121 1.518 1.00 98.34 9 A 1 ATOM 70 C CA . SER A 1 9 ? 2.763 0.471 0.270 1.00 98.31 9 A 1 ATOM 71 C C . SER A 1 9 ? 2.827 1.485 -0.866 1.00 98.44 9 A 1 ATOM 72 O O . SER A 1 9 ? 3.702 1.418 -1.729 1.00 98.14 9 A 1 ATOM 73 C CB . SER A 1 9 ? 1.779 -0.638 -0.072 1.00 97.92 9 A 1 ATOM 74 O OG . SER A 1 9 ? 2.455 -1.739 -0.639 1.00 93.53 9 A 1 ATOM 75 N N . PHE A 1 10 ? 1.893 2.429 -0.852 1.00 98.58 10 A 1 ATOM 76 C CA . PHE A 1 10 ? 1.835 3.473 -1.875 1.00 98.49 10 A 1 ATOM 77 C C . PHE A 1 10 ? 3.045 4.398 -1.760 1.00 98.58 10 A 1 ATOM 78 O O . PHE A 1 10 ? 3.607 4.831 -2.767 1.00 98.29 10 A 1 ATOM 79 C CB . PHE A 1 10 ? 0.544 4.274 -1.710 1.00 98.22 10 A 1 ATOM 80 C CG . PHE A 1 10 ? 0.069 4.882 -3.005 1.00 96.87 10 A 1 ATOM 81 C CD1 . PHE A 1 10 ? 0.661 6.026 -3.509 1.00 94.46 10 A 1 ATOM 82 C CD2 . PHE A 1 10 ? -0.972 4.291 -3.710 1.00 94.70 10 A 1 ATOM 83 C CE1 . PHE A 1 10 ? 0.232 6.585 -4.704 1.00 93.64 10 A 1 ATOM 84 C CE2 . PHE A 1 10 ? -1.409 4.847 -4.906 1.00 93.73 10 A 1 ATOM 85 C CZ . PHE A 1 10 ? -0.807 5.990 -5.403 1.00 93.75 10 A 1 ATOM 86 N N . ALA A 1 11 ? 3.443 4.697 -0.537 1.00 98.52 11 A 1 ATOM 87 C CA . ALA A 1 11 ? 4.586 5.577 -0.295 1.00 98.48 11 A 1 ATOM 88 C C . ALA A 1 11 ? 5.882 4.943 -0.792 1.00 98.56 11 A 1 ATOM 89 O O . ALA A 1 11 ? 6.723 5.622 -1.379 1.00 98.26 11 A 1 ATOM 90 C CB . ALA A 1 11 ? 4.689 5.890 1.189 1.00 98.24 11 A 1 ATOM 91 N N . ILE A 1 12 ? 6.040 3.649 -0.569 1.00 98.63 12 A 1 ATOM 92 C CA . ILE A 1 12 ? 7.231 2.926 -1.012 1.00 98.48 12 A 1 ATOM 93 C C . ILE A 1 12 ? 7.286 2.841 -2.532 1.00 98.50 12 A 1 ATOM 94 O O . ILE A 1 12 ? 8.348 3.009 -3.137 1.00 98.23 12 A 1 ATOM 95 C CB . ILE A 1 12 ? 7.255 1.513 -0.402 1.00 98.09 12 A 1 ATOM 96 C CG1 . ILE A 1 12 ? 7.364 1.588 1.118 1.00 96.72 12 A 1 ATOM 97 C CG2 . ILE A 1 12 ? 8.436 0.716 -0.972 1.00 96.52 12 A 1 ATOM 98 C CD1 . ILE A 1 12 ? 6.936 0.305 1.799 1.00 92.55 12 A 1 ATOM 99 N N . CYS A 1 13 ? 6.140 2.587 -3.144 1.00 98.46 13 A 1 ATOM 100 C CA . CYS A 1 13 ? 6.049 2.487 -4.597 1.00 98.27 13 A 1 ATOM 101 C C . CYS A 1 13 ? 6.355 3.834 -5.253 1.00 98.22 13 A 1 ATOM 102 O O . CYS A 1 13 ? 7.000 3.893 -6.299 1.00 97.15 13 A 1 ATOM 103 C CB . CYS A 1 13 ? 4.656 2.006 -5.000 1.00 97.40 13 A 1 ATOM 104 S SG . CYS A 1 13 ? 4.703 0.765 -6.317 1.00 91.54 13 A 1 ATOM 105 N N . ALA A 1 14 ? 5.875 4.912 -4.643 1.00 98.30 14 A 1 ATOM 106 C CA . ALA A 1 14 ? 6.087 6.263 -5.163 1.00 98.18 14 A 1 ATOM 107 C C . ALA A 1 14 ? 7.502 6.750 -4.883 1.00 98.23 14 A 1 ATOM 108 O O . ALA A 1 14 ? 8.071 7.499 -5.675 1.00 97.50 14 A 1 ATOM 109 C CB . ALA A 1 14 ? 5.075 7.218 -4.546 1.00 97.48 14 A 1 ATOM 110 N N . SER A 1 15 ? 8.060 6.339 -3.760 1.00 97.78 15 A 1 ATOM 111 C CA . SER A 1 15 ? 9.414 6.737 -3.371 1.00 97.52 15 A 1 ATOM 112 C C . SER A 1 15 ? 10.456 6.024 -4.220 1.00 96.98 15 A 1 ATOM 113 O O . SER A 1 15 ? 11.478 6.605 -4.591 1.00 93.17 15 A 1 ATOM 114 C CB . SER A 1 15 ? 9.647 6.443 -1.893 1.00 96.17 15 A 1 ATOM 115 O OG . SER A 1 15 ? 10.349 7.499 -1.284 1.00 89.00 15 A 1 ATOM 116 N N . GLY A 1 16 ? 10.176 4.780 -4.536 1.00 94.90 16 A 1 ATOM 117 C CA . GLY A 1 16 ? 11.087 3.980 -5.349 1.00 91.18 16 A 1 ATOM 118 C C . GLY A 1 16 ? 12.081 3.223 -4.484 1.00 88.22 16 A 1 ATOM 119 O O . GLY A 1 16 ? 12.729 3.835 -3.631 1.00 82.29 16 A 1 ATOM 120 O OXT . GLY A 1 16 ? 12.175 1.977 -4.653 1.00 87.47 16 A 1 #