# 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_spkb19288 # _entry.id spkb19288 # 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" "C2 H5 N O2" 75.067 GLY y GLYCINE C(C(=O)O)N ? "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" "C5 H9 N O2" 115.130 PRO y PROLINE C1C[C@H](NC1)C(=O)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" "C11 H12 N2 O2" 204.225 TRP y TRYPTOPHAN c1ccc2c(c1)c(c[nH]2)C[C@@H](C(=O)O)N ? "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 TRP 3 1 n VAL 4 1 n LEU 5 1 n VAL 6 1 n GLY 7 1 n THR 8 1 n VAL 9 1 n LEU 10 1 n PRO 11 1 n VAL 12 1 n MET 13 1 n LEU 14 1 n LEU 15 1 n ALA 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 20:48:53)" _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 91.25 _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 83.13 1 1 A LEU 2 2 88.44 1 2 A TRP 3 2 89.33 1 3 A VAL 4 2 93.34 1 4 A LEU 5 2 90.84 1 5 A VAL 6 2 92.31 1 6 A GLY 7 2 95.82 1 7 A THR 8 2 93.01 1 8 A VAL 9 2 93.92 1 9 A LEU 10 2 92.25 1 10 A PRO 11 2 95.08 1 11 A VAL 12 2 93.48 1 12 A MET 13 2 90.21 1 13 A LEU 14 2 92.93 1 14 A LEU 15 2 91.64 1 15 A ALA 16 2 89.20 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 TRP . 3 A 3 A 4 1 n VAL . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n VAL . 6 A 6 A 7 1 n GLY . 7 A 7 A 8 1 n THR . 8 A 8 A 9 1 n VAL . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n PRO . 11 A 11 A 12 1 n VAL . 12 A 12 A 13 1 n MET . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n LEU . 15 A 15 A 16 1 n ALA . 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 ? 2.715 -10.622 3.956 1.00 88.43 1 A 1 ATOM 2 C CA . MET A 1 1 ? 2.083 -9.320 4.215 1.00 88.99 1 A 1 ATOM 3 C C . MET A 1 1 ? 1.745 -8.594 2.912 1.00 90.66 1 A 1 ATOM 4 O O . MET A 1 1 ? 1.898 -7.379 2.805 1.00 88.73 1 A 1 ATOM 5 C CB . MET A 1 1 ? 3.004 -8.443 5.061 1.00 84.37 1 A 1 ATOM 6 C CG . MET A 1 1 ? 3.144 -8.918 6.491 1.00 79.09 1 A 1 ATOM 7 S SD . MET A 1 1 ? 4.190 -7.819 7.459 1.00 76.39 1 A 1 ATOM 8 C CE . MET A 1 1 ? 3.966 -8.509 9.087 1.00 68.36 1 A 1 ATOM 9 N N . LEU A 1 2 ? 1.280 -9.349 1.933 1.00 89.82 2 A 1 ATOM 10 C CA . LEU A 1 2 ? 0.917 -8.783 0.639 1.00 91.58 2 A 1 ATOM 11 C C . LEU A 1 2 ? -0.355 -7.946 0.740 1.00 93.83 2 A 1 ATOM 12 O O . LEU A 1 2 ? -0.507 -6.940 0.045 1.00 92.26 2 A 1 ATOM 13 C CB . LEU A 1 2 ? 0.743 -9.907 -0.391 1.00 89.91 2 A 1 ATOM 14 C CG . LEU A 1 2 ? -0.326 -10.943 -0.052 1.00 86.27 2 A 1 ATOM 15 C CD1 . LEU A 1 2 ? -1.586 -10.677 -0.867 1.00 83.17 2 A 1 ATOM 16 C CD2 . LEU A 1 2 ? 0.193 -12.342 -0.327 1.00 80.68 2 A 1 ATOM 17 N N . TRP A 1 3 ? -1.274 -8.379 1.626 1.00 91.89 3 A 1 ATOM 18 C CA . TRP A 1 3 ? -2.534 -7.664 1.835 1.00 93.01 3 A 1 ATOM 19 C C . TRP A 1 3 ? -2.271 -6.290 2.436 1.00 94.13 3 A 1 ATOM 20 O O . TRP A 1 3 ? -2.905 -5.297 2.066 1.00 92.89 3 A 1 ATOM 21 C CB . TRP A 1 3 ? -3.459 -8.459 2.760 1.00 91.96 3 A 1 ATOM 22 C CG . TRP A 1 3 ? -3.185 -9.931 2.815 1.00 90.14 3 A 1 ATOM 23 C CD1 . TRP A 1 3 ? -2.160 -10.551 3.451 1.00 88.18 3 A 1 ATOM 24 C CD2 . TRP A 1 3 ? -3.973 -10.975 2.201 1.00 89.79 3 A 1 ATOM 25 N NE1 . TRP A 1 3 ? -2.247 -11.918 3.271 1.00 86.58 3 A 1 ATOM 26 C CE2 . TRP A 1 3 ? -3.355 -12.201 2.505 1.00 88.45 3 A 1 ATOM 27 C CE3 . TRP A 1 3 ? -5.139 -10.975 1.438 1.00 87.51 3 A 1 ATOM 28 C CZ2 . TRP A 1 3 ? -3.872 -13.419 2.062 1.00 87.14 3 A 1 ATOM 29 C CZ3 . TRP A 1 3 ? -5.654 -12.190 1.002 1.00 84.52 3 A 1 ATOM 30 C CH2 . TRP A 1 3 ? -5.021 -13.397 1.308 1.00 84.43 3 A 1 ATOM 31 N N . VAL A 1 4 ? -1.318 -6.236 3.359 1.00 94.17 4 A 1 ATOM 32 C CA . VAL A 1 4 ? -0.946 -4.991 4.023 1.00 95.04 4 A 1 ATOM 33 C C . VAL A 1 4 ? -0.293 -4.029 3.037 1.00 95.41 4 A 1 ATOM 34 O O . VAL A 1 4 ? -0.544 -2.822 3.075 1.00 94.24 4 A 1 ATOM 35 C CB . VAL A 1 4 ? 0.008 -5.254 5.204 1.00 94.32 4 A 1 ATOM 36 C CG1 . VAL A 1 4 ? 0.332 -3.957 5.930 1.00 90.13 4 A 1 ATOM 37 C CG2 . VAL A 1 4 ? -0.600 -6.259 6.174 1.00 90.08 4 A 1 ATOM 38 N N . LEU A 1 5 ? 0.543 -4.561 2.162 1.00 92.46 5 A 1 ATOM 39 C CA . LEU A 1 5 ? 1.233 -3.760 1.155 1.00 92.90 5 A 1 ATOM 40 C C . LEU A 1 5 ? 0.241 -3.095 0.208 1.00 94.05 5 A 1 ATOM 41 O O . LEU A 1 5 ? 0.328 -1.895 -0.060 1.00 93.57 5 A 1 ATOM 42 C CB . LEU A 1 5 ? 2.203 -4.636 0.361 1.00 92.18 5 A 1 ATOM 43 C CG . LEU A 1 5 ? 3.593 -4.784 0.978 1.00 89.01 5 A 1 ATOM 44 C CD1 . LEU A 1 5 ? 4.327 -5.970 0.367 1.00 86.74 5 A 1 ATOM 45 C CD2 . LEU A 1 5 ? 4.397 -3.511 0.775 1.00 85.78 5 A 1 ATOM 46 N N . VAL A 1 6 ? -0.707 -3.874 -0.293 1.00 93.56 6 A 1 ATOM 47 C CA . VAL A 1 6 ? -1.726 -3.368 -1.210 1.00 93.77 6 A 1 ATOM 48 C C . VAL A 1 6 ? -2.658 -2.391 -0.506 1.00 94.48 6 A 1 ATOM 49 O O . VAL A 1 6 ? -3.059 -1.374 -1.080 1.00 93.88 6 A 1 ATOM 50 C CB . VAL A 1 6 ? -2.549 -4.521 -1.813 1.00 92.61 6 A 1 ATOM 51 C CG1 . VAL A 1 6 ? -3.601 -3.986 -2.772 1.00 88.48 6 A 1 ATOM 52 C CG2 . VAL A 1 6 ? -1.641 -5.511 -2.526 1.00 89.39 6 A 1 ATOM 53 N N . GLY A 1 7 ? -3.001 -2.706 0.732 1.00 95.66 7 A 1 ATOM 54 C CA . GLY A 1 7 ? -3.891 -1.861 1.520 1.00 95.71 7 A 1 ATOM 55 C C . GLY A 1 7 ? -3.231 -0.588 2.006 1.00 96.50 7 A 1 ATOM 56 O O . GLY A 1 7 ? -3.911 0.350 2.419 1.00 95.42 7 A 1 ATOM 57 N N . THR A 1 8 ? -1.910 -0.558 1.970 1.00 94.38 8 A 1 ATOM 58 C CA . THR A 1 8 ? -1.149 0.612 2.405 1.00 94.57 8 A 1 ATOM 59 C C . THR A 1 8 ? -0.810 1.521 1.228 1.00 95.43 8 A 1 ATOM 60 O O . THR A 1 8 ? -0.837 2.746 1.354 1.00 93.97 8 A 1 ATOM 61 C CB . THR A 1 8 ? 0.150 0.194 3.110 1.00 93.44 8 A 1 ATOM 62 O OG1 . THR A 1 8 ? -0.138 -0.751 4.135 1.00 89.86 8 A 1 ATOM 63 C CG2 . THR A 1 8 ? 0.839 1.395 3.733 1.00 89.39 8 A 1 ATOM 64 N N . VAL A 1 9 ? -0.496 0.923 0.097 1.00 95.20 9 A 1 ATOM 65 C CA . VAL A 1 9 ? -0.138 1.679 -1.099 1.00 95.19 9 A 1 ATOM 66 C C . VAL A 1 9 ? -1.330 2.475 -1.624 1.00 95.59 9 A 1 ATOM 67 O O . VAL A 1 9 ? -1.176 3.608 -2.086 1.00 94.66 9 A 1 ATOM 68 C CB . VAL A 1 9 ? 0.396 0.755 -2.210 1.00 94.18 9 A 1 ATOM 69 C CG1 . VAL A 1 9 ? 0.650 1.537 -3.486 1.00 91.10 9 A 1 ATOM 70 C CG2 . VAL A 1 9 ? 1.663 0.055 -1.763 1.00 91.51 9 A 1 ATOM 71 N N . LEU A 1 10 ? -2.517 1.881 -1.541 1.00 94.95 10 A 1 ATOM 72 C CA . LEU A 1 10 ? -3.737 2.534 -2.007 1.00 94.59 10 A 1 ATOM 73 C C . LEU A 1 10 ? -4.007 3.852 -1.278 1.00 95.61 10 A 1 ATOM 74 O O . LEU A 1 10 ? -4.142 4.895 -1.926 1.00 95.27 10 A 1 ATOM 75 C CB . LEU A 1 10 ? -4.931 1.592 -1.858 1.00 93.81 10 A 1 ATOM 76 C CG . LEU A 1 10 ? -5.331 0.860 -3.134 1.00 89.16 10 A 1 ATOM 77 C CD1 . LEU A 1 10 ? -6.222 -0.331 -2.811 1.00 87.57 10 A 1 ATOM 78 C CD2 . LEU A 1 10 ? -6.033 1.802 -4.091 1.00 87.05 10 A 1 ATOM 79 N N . PRO A 1 11 ? -4.109 3.819 0.062 1.00 95.83 11 A 1 ATOM 80 C CA . PRO A 1 11 ? -4.373 5.040 0.836 1.00 95.56 11 A 1 ATOM 81 C C . PRO A 1 11 ? -3.242 6.046 0.739 1.00 96.18 11 A 1 ATOM 82 O O . PRO A 1 11 ? -3.486 7.253 0.778 1.00 95.21 11 A 1 ATOM 83 C CB . PRO A 1 11 ? -4.527 4.532 2.272 1.00 94.28 11 A 1 ATOM 84 C CG . PRO A 1 11 ? -3.809 3.232 2.292 1.00 92.96 11 A 1 ATOM 85 C CD . PRO A 1 11 ? -3.997 2.647 0.921 1.00 95.53 11 A 1 ATOM 86 N N . VAL A 1 12 ? -2.015 5.568 0.614 1.00 94.90 12 A 1 ATOM 87 C CA . VAL A 1 12 ? -0.854 6.444 0.501 1.00 95.02 12 A 1 ATOM 88 C C . VAL A 1 12 ? -0.873 7.184 -0.832 1.00 95.49 12 A 1 ATOM 89 O O . VAL A 1 12 ? -0.492 8.353 -0.910 1.00 94.31 12 A 1 ATOM 90 C CB . VAL A 1 12 ? 0.457 5.652 0.644 1.00 93.96 12 A 1 ATOM 91 C CG1 . VAL A 1 12 ? 1.658 6.532 0.333 1.00 90.11 12 A 1 ATOM 92 C CG2 . VAL A 1 12 ? 0.578 5.079 2.040 1.00 90.57 12 A 1 ATOM 93 N N . MET A 1 13 ? -1.327 6.501 -1.870 1.00 95.20 13 A 1 ATOM 94 C CA . MET A 1 13 ? -1.391 7.081 -3.208 1.00 94.65 13 A 1 ATOM 95 C C . MET A 1 13 ? -2.458 8.165 -3.295 1.00 95.62 13 A 1 ATOM 96 O O . MET A 1 13 ? -2.255 9.192 -3.939 1.00 94.24 13 A 1 ATOM 97 C CB . MET A 1 13 ? -1.674 6.001 -4.250 1.00 93.55 13 A 1 ATOM 98 C CG . MET A 1 13 ? -1.139 6.362 -5.627 1.00 89.24 13 A 1 ATOM 99 S SD . MET A 1 13 ? 0.647 6.309 -5.680 1.00 83.60 13 A 1 ATOM 100 C CE . MET A 1 13 ? 0.951 7.003 -7.297 1.00 75.61 13 A 1 ATOM 101 N N . LEU A 1 14 ? -3.603 7.924 -2.648 1.00 94.58 14 A 1 ATOM 102 C CA . LEU A 1 14 ? -4.694 8.889 -2.654 1.00 94.73 14 A 1 ATOM 103 C C . LEU A 1 14 ? -4.362 10.102 -1.796 1.00 95.55 14 A 1 ATOM 104 O O . LEU A 1 14 ? -4.822 11.215 -2.076 1.00 94.54 14 A 1 ATOM 105 C CB . LEU A 1 14 ? -5.990 8.227 -2.159 1.00 94.52 14 A 1 ATOM 106 C CG . LEU A 1 14 ? -6.056 7.949 -0.658 1.00 92.10 14 A 1 ATOM 107 C CD1 . LEU A 1 14 ? -6.713 9.106 0.084 1.00 89.22 14 A 1 ATOM 108 C CD2 . LEU A 1 14 ? -6.826 6.671 -0.397 1.00 88.19 14 A 1 ATOM 109 N N . LEU A 1 15 ? -3.574 9.883 -0.743 1.00 94.87 15 A 1 ATOM 110 C CA . LEU A 1 15 ? -3.165 10.958 0.151 1.00 94.56 15 A 1 ATOM 111 C C . LEU A 1 15 ? -2.065 11.804 -0.469 1.00 94.81 15 A 1 ATOM 112 O O . LEU A 1 15 ? -2.115 13.038 -0.429 1.00 93.01 15 A 1 ATOM 113 C CB . LEU A 1 15 ? -2.692 10.382 1.490 1.00 93.59 15 A 1 ATOM 114 C CG . LEU A 1 15 ? -3.804 10.035 2.475 1.00 90.63 15 A 1 ATOM 115 C CD1 . LEU A 1 15 ? -3.308 9.073 3.540 1.00 86.86 15 A 1 ATOM 116 C CD2 . LEU A 1 15 ? -4.336 11.307 3.124 1.00 84.79 15 A 1 ATOM 117 N N . ALA A 1 16 ? -1.065 11.128 -1.019 1.00 94.02 16 A 1 ATOM 118 C CA . ALA A 1 16 ? 0.064 11.801 -1.636 1.00 92.47 16 A 1 ATOM 119 C C . ALA A 1 16 ? -0.185 12.080 -3.117 1.00 90.81 16 A 1 ATOM 120 O O . ALA A 1 16 ? -0.951 11.339 -3.753 1.00 87.90 16 A 1 ATOM 121 C CB . ALA A 1 16 ? 1.335 10.981 -1.454 1.00 88.81 16 A 1 ATOM 122 O OXT . ALA A 1 16 ? 0.397 13.032 -3.653 1.00 81.20 16 A 1 #