# 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_spkb37346 # _entry.id spkb37346 # 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 S" 121.158 CYS y CYSTEINE C([C@@H](C(=O)O)N)S ? "L-PEPTIDE LINKING" "C5 H9 N O4" 147.129 GLU y "GLUTAMIC ACID" C(CC(=O)O)[C@@H](C(=O)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" "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" "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 MET 1 1 n LEU 2 1 n LYS 3 1 n LEU 4 1 n VAL 5 1 n ILE 6 1 n LEU 7 1 n LEU 8 1 n CYS 9 1 n VAL 10 1 n ILE 11 1 n GLU 12 1 n SER 13 1 n ILE 14 1 n TYR 15 1 n SER 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 @ 2025-07-07 10:55:42)" _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 95.63 _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 89.39 1 1 A LEU 2 2 94.95 1 2 A LYS 3 2 94.29 1 3 A LEU 4 2 96.33 1 4 A VAL 5 2 97.79 1 5 A ILE 6 2 97.76 1 6 A LEU 7 2 96.81 1 7 A LEU 8 2 96.11 1 8 A CYS 9 2 97.31 1 9 A VAL 10 2 98.25 1 10 A ILE 11 2 97.74 1 11 A GLU 12 2 92.67 1 12 A SER 13 2 96.91 1 13 A ILE 14 2 98.00 1 14 A TYR 15 2 95.68 1 15 A SER 16 2 91.38 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 LEU . 2 A 2 A 3 1 n LYS . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n ILE . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n CYS . 9 A 9 A 10 1 n VAL . 10 A 10 A 11 1 n ILE . 11 A 11 A 12 1 n GLU . 12 A 12 A 13 1 n SER . 13 A 13 A 14 1 n ILE . 14 A 14 A 15 1 n TYR . 15 A 15 A 16 1 n SER . 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 ? 3.680 11.214 7.374 1.00 95.04 1 A 1 ATOM 2 C CA . MET A 1 1 ? 2.574 10.836 6.471 1.00 96.37 1 A 1 ATOM 3 C C . MET A 1 1 ? 2.963 9.688 5.537 1.00 96.33 1 A 1 ATOM 4 O O . MET A 1 1 ? 2.101 8.994 5.007 1.00 94.58 1 A 1 ATOM 5 C CB . MET A 1 1 ? 2.123 12.028 5.616 1.00 93.95 1 A 1 ATOM 6 C CG . MET A 1 1 ? 1.229 13.011 6.394 1.00 86.01 1 A 1 ATOM 7 S SD . MET A 1 1 ? 2.129 14.325 7.159 1.00 80.96 1 A 1 ATOM 8 C CE . MET A 1 1 ? 0.779 15.300 7.842 1.00 71.84 1 A 1 ATOM 9 N N . LEU A 1 2 ? 4.254 9.498 5.345 1.00 96.81 2 A 1 ATOM 10 C CA . LEU A 1 2 ? 4.743 8.432 4.470 1.00 97.57 2 A 1 ATOM 11 C C . LEU A 1 2 ? 4.298 7.053 4.948 1.00 98.09 2 A 1 ATOM 12 O O . LEU A 1 2 ? 4.064 6.149 4.139 1.00 97.72 2 A 1 ATOM 13 C CB . LEU A 1 2 ? 6.271 8.488 4.376 1.00 96.89 2 A 1 ATOM 14 C CG . LEU A 1 2 ? 6.904 7.418 3.492 1.00 92.41 2 A 1 ATOM 15 C CD1 . LEU A 1 2 ? 6.405 7.539 2.056 1.00 90.17 2 A 1 ATOM 16 C CD2 . LEU A 1 2 ? 8.418 7.534 3.531 1.00 89.94 2 A 1 ATOM 17 N N . LYS A 1 3 ? 4.157 6.904 6.265 1.00 98.17 3 A 1 ATOM 18 C CA . LYS A 1 3 ? 3.747 5.625 6.844 1.00 98.43 3 A 1 ATOM 19 C C . LYS A 1 3 ? 2.380 5.180 6.324 1.00 98.49 3 A 1 ATOM 20 O O . LYS A 1 3 ? 2.118 3.980 6.212 1.00 98.21 3 A 1 ATOM 21 C CB . LYS A 1 3 ? 3.734 5.711 8.377 1.00 98.10 3 A 1 ATOM 22 C CG . LYS A 1 3 ? 3.014 6.935 8.914 1.00 94.29 3 A 1 ATOM 23 C CD . LYS A 1 3 ? 3.047 6.984 10.433 1.00 92.25 3 A 1 ATOM 24 C CE . LYS A 1 3 ? 2.568 8.332 10.963 1.00 88.25 3 A 1 ATOM 25 N NZ . LYS A 1 3 ? 3.523 9.417 10.623 1.00 82.46 3 A 1 ATOM 26 N N . LEU A 1 4 ? 1.519 6.138 5.987 1.00 98.20 4 A 1 ATOM 27 C CA . LEU A 1 4 ? 0.201 5.825 5.443 1.00 98.40 4 A 1 ATOM 28 C C . LEU A 1 4 ? 0.322 5.258 4.033 1.00 98.57 4 A 1 ATOM 29 O O . LEU A 1 4 ? -0.427 4.359 3.648 1.00 98.42 4 A 1 ATOM 30 C CB . LEU A 1 4 ? -0.690 7.075 5.430 1.00 98.24 4 A 1 ATOM 31 C CG . LEU A 1 4 ? -1.012 7.658 6.808 1.00 93.95 4 A 1 ATOM 32 C CD1 . LEU A 1 4 ? -1.886 8.896 6.667 1.00 91.98 4 A 1 ATOM 33 C CD2 . LEU A 1 4 ? -1.706 6.625 7.686 1.00 92.87 4 A 1 ATOM 34 N N . VAL A 1 5 ? 1.267 5.781 3.265 1.00 98.53 5 A 1 ATOM 35 C CA . VAL A 1 5 ? 1.514 5.301 1.908 1.00 98.55 5 A 1 ATOM 36 C C . VAL A 1 5 ? 2.040 3.870 1.955 1.00 98.61 5 A 1 ATOM 37 O O . VAL A 1 5 ? 1.625 3.016 1.165 1.00 98.30 5 A 1 ATOM 38 C CB . VAL A 1 5 ? 2.513 6.213 1.169 1.00 98.27 5 A 1 ATOM 39 C CG1 . VAL A 1 5 ? 2.793 5.687 -0.232 1.00 96.02 5 A 1 ATOM 40 C CG2 . VAL A 1 5 ? 1.972 7.639 1.101 1.00 96.22 5 A 1 ATOM 41 N N . ILE A 1 6 ? 2.947 3.609 2.891 1.00 98.62 6 A 1 ATOM 42 C CA . ILE A 1 6 ? 3.511 2.272 3.063 1.00 98.61 6 A 1 ATOM 43 C C . ILE A 1 6 ? 2.412 1.278 3.427 1.00 98.58 6 A 1 ATOM 44 O O . ILE A 1 6 ? 2.354 0.176 2.879 1.00 98.41 6 A 1 ATOM 45 C CB . ILE A 1 6 ? 4.609 2.276 4.149 1.00 98.59 6 A 1 ATOM 46 C CG1 . ILE A 1 6 ? 5.776 3.192 3.736 1.00 97.61 6 A 1 ATOM 47 C CG2 . ILE A 1 6 ? 5.106 0.857 4.417 1.00 97.27 6 A 1 ATOM 48 C CD1 . ILE A 1 6 ? 6.467 2.751 2.454 1.00 94.37 6 A 1 ATOM 49 N N . LEU A 1 7 ? 1.537 1.669 4.335 1.00 98.73 7 A 1 ATOM 50 C CA . LEU A 1 7 ? 0.427 0.819 4.753 1.00 98.68 7 A 1 ATOM 51 C C . LEU A 1 7 ? -0.484 0.492 3.573 1.00 98.67 7 A 1 ATOM 52 O O . LEU A 1 7 ? -0.919 -0.649 3.413 1.00 98.52 7 A 1 ATOM 53 C CB . LEU A 1 7 ? -0.373 1.511 5.859 1.00 98.54 7 A 1 ATOM 54 C CG . LEU A 1 7 ? -1.581 0.729 6.372 1.00 94.44 7 A 1 ATOM 55 C CD1 . LEU A 1 7 ? -1.144 -0.622 6.931 1.00 92.51 7 A 1 ATOM 56 C CD2 . LEU A 1 7 ? -2.320 1.526 7.432 1.00 94.41 7 A 1 ATOM 57 N N . LEU A 1 8 ? -0.773 1.487 2.753 1.00 98.52 8 A 1 ATOM 58 C CA . LEU A 1 8 ? -1.613 1.296 1.577 1.00 98.45 8 A 1 ATOM 59 C C . LEU A 1 8 ? -0.977 0.301 0.614 1.00 98.51 8 A 1 ATOM 60 O O . LEU A 1 8 ? -1.660 -0.557 0.054 1.00 98.26 8 A 1 ATOM 61 C CB . LEU A 1 8 ? -1.840 2.638 0.869 1.00 98.16 8 A 1 ATOM 62 C CG . LEU A 1 8 ? -2.714 2.566 -0.385 1.00 92.92 8 A 1 ATOM 63 C CD1 . LEU A 1 8 ? -4.099 2.031 -0.057 1.00 91.31 8 A 1 ATOM 64 C CD2 . LEU A 1 8 ? -2.827 3.942 -1.027 1.00 92.74 8 A 1 ATOM 65 N N . CYS A 1 9 ? 0.338 0.405 0.422 1.00 98.35 9 A 1 ATOM 66 C CA . CYS A 1 9 ? 1.063 -0.504 -0.457 1.00 98.33 9 A 1 ATOM 67 C C . CYS A 1 9 ? 0.978 -1.943 0.047 1.00 98.38 9 A 1 ATOM 68 O O . CYS A 1 9 ? 0.818 -2.872 -0.740 1.00 97.79 9 A 1 ATOM 69 C CB . CYS A 1 9 ? 2.528 -0.073 -0.573 1.00 98.03 9 A 1 ATOM 70 S SG . CYS A 1 9 ? 2.751 1.486 -1.460 1.00 93.00 9 A 1 ATOM 71 N N . VAL A 1 10 ? 1.072 -2.122 1.358 1.00 98.69 10 A 1 ATOM 72 C CA . VAL A 1 10 ? 0.984 -3.446 1.966 1.00 98.65 10 A 1 ATOM 73 C C . VAL A 1 10 ? -0.410 -4.038 1.761 1.00 98.71 10 A 1 ATOM 74 O O . VAL A 1 10 ? -0.552 -5.216 1.428 1.00 98.46 10 A 1 ATOM 75 C CB . VAL A 1 10 ? 1.318 -3.389 3.467 1.00 98.46 10 A 1 ATOM 76 C CG1 . VAL A 1 10 ? 1.094 -4.749 4.118 1.00 97.13 10 A 1 ATOM 77 C CG2 . VAL A 1 10 ? 2.755 -2.944 3.677 1.00 97.68 10 A 1 ATOM 78 N N . ILE A 1 11 ? -1.432 -3.219 1.956 1.00 98.50 11 A 1 ATOM 79 C CA . ILE A 1 11 ? -2.814 -3.659 1.780 1.00 98.46 11 A 1 ATOM 80 C C . ILE A 1 11 ? -3.058 -4.093 0.335 1.00 98.46 11 A 1 ATOM 81 O O . ILE A 1 11 ? -3.659 -5.136 0.078 1.00 98.19 11 A 1 ATOM 82 C CB . ILE A 1 11 ? -3.800 -2.544 2.184 1.00 98.29 11 A 1 ATOM 83 C CG1 . ILE A 1 11 ? -3.705 -2.278 3.691 1.00 97.30 11 A 1 ATOM 84 C CG2 . ILE A 1 11 ? -5.232 -2.932 1.809 1.00 97.06 11 A 1 ATOM 85 C CD1 . ILE A 1 11 ? -4.475 -1.051 4.143 1.00 95.65 11 A 1 ATOM 86 N N . GLU A 1 12 ? -2.591 -3.289 -0.613 1.00 98.64 12 A 1 ATOM 87 C CA . GLU A 1 12 ? -2.745 -3.628 -2.028 1.00 98.55 12 A 1 ATOM 88 C C . GLU A 1 12 ? -1.972 -4.894 -2.379 1.00 98.58 12 A 1 ATOM 89 O O . GLU A 1 12 ? -2.379 -5.649 -3.263 1.00 98.04 12 A 1 ATOM 90 C CB . GLU A 1 12 ? -2.278 -2.470 -2.915 1.00 98.22 12 A 1 ATOM 91 C CG . GLU A 1 12 ? -3.188 -1.256 -2.839 1.00 91.51 12 A 1 ATOM 92 C CD . GLU A 1 12 ? -2.997 -0.336 -4.027 1.00 87.34 12 A 1 ATOM 93 O OE1 . GLU A 1 12 ? -2.055 0.477 -4.010 1.00 82.15 12 A 1 ATOM 94 O OE2 . GLU A 1 12 ? -3.787 -0.447 -4.982 1.00 81.02 12 A 1 ATOM 95 N N . SER A 1 13 ? -0.871 -5.135 -1.684 1.00 98.52 13 A 1 ATOM 96 C CA . SER A 1 13 ? -0.046 -6.316 -1.906 1.00 98.51 13 A 1 ATOM 97 C C . SER A 1 13 ? -0.776 -7.594 -1.497 1.00 98.62 13 A 1 ATOM 98 O O . SER A 1 13 ? -0.731 -8.598 -2.208 1.00 97.99 13 A 1 ATOM 99 C CB . SER A 1 13 ? 1.271 -6.193 -1.138 1.00 97.89 13 A 1 ATOM 100 O OG . SER A 1 13 ? 2.103 -7.301 -1.384 1.00 89.94 13 A 1 ATOM 101 N N . ILE A 1 14 ? -1.463 -7.558 -0.356 1.00 98.62 14 A 1 ATOM 102 C CA . ILE A 1 14 ? -2.191 -8.725 0.140 1.00 98.66 14 A 1 ATOM 103 C C . ILE A 1 14 ? -3.510 -8.932 -0.603 1.00 98.66 14 A 1 ATOM 104 O O . ILE A 1 14 ? -4.044 -10.038 -0.638 1.00 98.30 14 A 1 ATOM 105 C CB . ILE A 1 14 ? -2.456 -8.627 1.659 1.00 98.51 14 A 1 ATOM 106 C CG1 . ILE A 1 14 ? -3.319 -7.416 1.987 1.00 97.59 14 A 1 ATOM 107 C CG2 . ILE A 1 14 ? -1.137 -8.580 2.420 1.00 97.14 14 A 1 ATOM 108 C CD1 . ILE A 1 14 ? -3.699 -7.314 3.458 1.00 96.56 14 A 1 ATOM 109 N N . TYR A 1 15 ? -4.043 -7.865 -1.172 1.00 98.46 15 A 1 ATOM 110 C CA . TYR A 1 15 ? -5.298 -7.930 -1.917 1.00 98.38 15 A 1 ATOM 111 C C . TYR A 1 15 ? -5.068 -8.241 -3.397 1.00 98.20 15 A 1 ATOM 112 O O . TYR A 1 15 ? -6.028 -8.442 -4.142 1.00 97.32 15 A 1 ATOM 113 C CB . TYR A 1 15 ? -6.077 -6.612 -1.777 1.00 97.98 15 A 1 ATOM 114 C CG . TYR A 1 15 ? -6.907 -6.527 -0.510 1.00 96.34 15 A 1 ATOM 115 C CD1 . TYR A 1 15 ? -6.305 -6.451 0.736 1.00 93.99 15 A 1 ATOM 116 C CD2 . TYR A 1 15 ? -8.293 -6.525 -0.579 1.00 93.94 15 A 1 ATOM 117 C CE1 . TYR A 1 15 ? -7.059 -6.375 1.893 1.00 93.48 15 A 1 ATOM 118 C CE2 . TYR A 1 15 ? -9.063 -6.444 0.575 1.00 93.82 15 A 1 ATOM 119 C CZ . TYR A 1 15 ? -8.438 -6.370 1.808 1.00 93.96 15 A 1 ATOM 120 O OH . TYR A 1 15 ? -9.194 -6.290 2.950 1.00 92.30 15 A 1 ATOM 121 N N . SER A 1 16 ? -3.819 -8.278 -3.811 1.00 96.35 16 A 1 ATOM 122 C CA . SER A 1 16 ? -3.485 -8.538 -5.206 1.00 95.66 16 A 1 ATOM 123 C C . SER A 1 16 ? -3.632 -10.023 -5.543 1.00 93.67 16 A 1 ATOM 124 O O . SER A 1 16 ? -4.024 -10.345 -6.680 1.00 90.64 16 A 1 ATOM 125 C CB . SER A 1 16 ? -2.060 -8.054 -5.511 1.00 93.35 16 A 1 ATOM 126 O OG . SER A 1 16 ? -1.094 -8.808 -4.819 1.00 85.77 16 A 1 ATOM 127 O OXT . SER A 1 16 ? -3.330 -10.869 -4.729 1.00 84.20 16 A 1 #