# 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_spkb19123 # _entry.id spkb19123 # 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 "C6 H15 N4 O2" 175.209 ARG y ARGININE C(C[C@@H](C(=O)O)N)CNC(=[NH2+])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" "C4 H9 N O3" 119.119 THR y THREONINE C[C@H]([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 ARG 2 1 n LEU 3 1 n LEU 4 1 n ILE 5 1 n CYS 6 1 n LEU 7 1 n THR 8 1 n LEU 9 1 n LEU 10 1 n GLY 11 1 n LEU 12 1 n VAL 13 1 n CYS 14 1 n GLY 15 # _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 @ 2025-07-03 11:26:46)" _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 90.56 _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 83.30 1 1 A ARG 2 2 85.03 1 2 A LEU 3 2 90.32 1 3 A LEU 4 2 91.50 1 4 A ILE 5 2 92.04 1 5 A CYS 6 2 94.93 1 6 A LEU 7 2 94.46 1 7 A THR 8 2 94.80 1 8 A LEU 9 2 94.16 1 9 A LEU 10 2 93.93 1 10 A GLY 11 2 95.15 1 11 A LEU 12 2 91.91 1 12 A VAL 13 2 90.59 1 13 A CYS 14 2 90.54 1 14 A GLY 15 2 76.54 1 15 # _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 ARG . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n ILE . 5 A 5 A 6 1 n CYS . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n THR . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n GLY . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n VAL . 13 A 13 A 14 1 n CYS . 14 A 14 A 15 1 n GLY . 15 A 15 # _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 ? -5.622 4.647 10.398 1.00 86.02 1 A 1 ATOM 2 C CA . MET A 1 1 ? -5.313 4.900 8.985 1.00 88.06 1 A 1 ATOM 3 C C . MET A 1 1 ? -4.673 3.669 8.334 1.00 90.12 1 A 1 ATOM 4 O O . MET A 1 1 ? -3.550 3.303 8.640 1.00 87.61 1 A 1 ATOM 5 C CB . MET A 1 1 ? -4.369 6.091 8.867 1.00 85.33 1 A 1 ATOM 6 C CG . MET A 1 1 ? -3.126 5.950 9.723 1.00 81.77 1 A 1 ATOM 7 S SD . MET A 1 1 ? -2.121 7.435 9.746 1.00 79.21 1 A 1 ATOM 8 C CE . MET A 1 1 ? -3.164 8.490 10.728 1.00 68.25 1 A 1 ATOM 9 N N . ARG A 1 2 ? -5.415 3.035 7.432 1.00 89.44 2 A 1 ATOM 10 C CA . ARG A 1 2 ? -4.943 1.837 6.739 1.00 91.24 2 A 1 ATOM 11 C C . ARG A 1 2 ? -4.008 2.173 5.588 1.00 93.26 2 A 1 ATOM 12 O O . ARG A 1 2 ? -3.344 1.297 5.045 1.00 91.53 2 A 1 ATOM 13 C CB . ARG A 1 2 ? -6.138 1.040 6.224 1.00 89.44 2 A 1 ATOM 14 C CG . ARG A 1 2 ? -7.180 1.905 5.549 1.00 85.93 2 A 1 ATOM 15 C CD . ARG A 1 2 ? -6.826 2.204 4.107 1.00 85.12 2 A 1 ATOM 16 N NE . ARG A 1 2 ? -7.030 1.035 3.246 1.00 80.96 2 A 1 ATOM 17 C CZ . ARG A 1 2 ? -6.859 1.042 1.937 1.00 80.83 2 A 1 ATOM 18 N NH1 . ARG A 1 2 ? -6.463 2.142 1.329 1.00 73.67 2 A 1 ATOM 19 N NH2 . ARG A 1 2 ? -7.085 -0.057 1.234 1.00 73.95 2 A 1 ATOM 20 N N . LEU A 1 3 ? -3.975 3.437 5.213 1.00 91.41 3 A 1 ATOM 21 C CA . LEU A 1 3 ? -3.127 3.888 4.112 1.00 92.81 3 A 1 ATOM 22 C C . LEU A 1 3 ? -1.659 3.625 4.408 1.00 94.60 3 A 1 ATOM 23 O O . LEU A 1 3 ? -0.864 3.423 3.498 1.00 93.23 3 A 1 ATOM 24 C CB . LEU A 1 3 ? -3.340 5.382 3.870 1.00 92.15 3 A 1 ATOM 25 C CG . LEU A 1 3 ? -4.766 5.750 3.476 1.00 88.39 3 A 1 ATOM 26 C CD1 . LEU A 1 3 ? -4.893 7.255 3.329 1.00 85.09 3 A 1 ATOM 27 C CD2 . LEU A 1 3 ? -5.155 5.059 2.181 1.00 84.90 3 A 1 ATOM 28 N N . LEU A 1 4 ? -1.314 3.640 5.673 1.00 93.34 4 A 1 ATOM 29 C CA . LEU A 1 4 ? 0.063 3.394 6.087 1.00 93.89 4 A 1 ATOM 30 C C . LEU A 1 4 ? 0.524 2.025 5.611 1.00 94.99 4 A 1 ATOM 31 O O . LEU A 1 4 ? 1.668 1.843 5.203 1.00 93.95 4 A 1 ATOM 32 C CB . LEU A 1 4 ? 0.172 3.507 7.606 1.00 93.26 4 A 1 ATOM 33 C CG . LEU A 1 4 ? 1.597 3.391 8.139 1.00 89.62 4 A 1 ATOM 34 C CD1 . LEU A 1 4 ? 1.755 4.243 9.385 1.00 86.94 4 A 1 ATOM 35 C CD2 . LEU A 1 4 ? 1.925 1.947 8.473 1.00 86.05 4 A 1 ATOM 36 N N . ILE A 1 5 ? -0.371 1.064 5.646 1.00 94.29 5 A 1 ATOM 37 C CA . ILE A 1 5 ? -0.056 -0.290 5.216 1.00 93.98 5 A 1 ATOM 38 C C . ILE A 1 5 ? 0.160 -0.324 3.713 1.00 94.43 5 A 1 ATOM 39 O O . ILE A 1 5 ? 1.022 -1.045 3.209 1.00 93.31 5 A 1 ATOM 40 C CB . ILE A 1 5 ? -1.180 -1.254 5.605 1.00 93.30 5 A 1 ATOM 41 C CG1 . ILE A 1 5 ? -1.389 -1.232 7.116 1.00 90.31 5 A 1 ATOM 42 C CG2 . ILE A 1 5 ? -0.843 -2.660 5.131 1.00 90.03 5 A 1 ATOM 43 C CD1 . ILE A 1 5 ? -2.563 -2.066 7.566 1.00 86.64 5 A 1 ATOM 44 N N . CYS A 1 6 ? -0.632 0.455 2.999 1.00 95.84 6 A 1 ATOM 45 C CA . CYS A 1 6 ? -0.506 0.533 1.547 1.00 95.75 6 A 1 ATOM 46 C C . CYS A 1 6 ? 0.893 0.979 1.148 1.00 95.92 6 A 1 ATOM 47 O O . CYS A 1 6 ? 1.526 0.380 0.286 1.00 94.60 6 A 1 ATOM 48 C CB . CYS A 1 6 ? -1.527 1.512 0.983 1.00 94.78 6 A 1 ATOM 49 S SG . CYS A 1 6 ? -1.045 2.181 -0.632 1.00 92.71 6 A 1 ATOM 50 N N . LEU A 1 7 ? 1.362 2.043 1.793 1.00 96.29 7 A 1 ATOM 51 C CA . LEU A 1 7 ? 2.685 2.581 1.503 1.00 96.34 7 A 1 ATOM 52 C C . LEU A 1 7 ? 3.761 1.544 1.767 1.00 96.95 7 A 1 ATOM 53 O O . LEU A 1 7 ? 4.771 1.488 1.068 1.00 96.09 7 A 1 ATOM 54 C CB . LEU A 1 7 ? 2.937 3.815 2.366 1.00 95.58 7 A 1 ATOM 55 C CG . LEU A 1 7 ? 1.939 4.947 2.127 1.00 93.59 7 A 1 ATOM 56 C CD1 . LEU A 1 7 ? 2.208 6.093 3.088 1.00 91.03 7 A 1 ATOM 57 C CD2 . LEU A 1 7 ? 2.018 5.433 0.693 1.00 89.79 7 A 1 ATOM 58 N N . THR A 1 8 ? 3.522 0.741 2.775 1.00 96.24 8 A 1 ATOM 59 C CA . THR A 1 8 ? 4.476 -0.304 3.137 1.00 96.08 8 A 1 ATOM 60 C C . THR A 1 8 ? 4.402 -1.462 2.153 1.00 96.49 8 A 1 ATOM 61 O O . THR A 1 8 ? 5.410 -2.098 1.847 1.00 95.44 8 A 1 ATOM 62 C CB . THR A 1 8 ? 4.190 -0.827 4.545 1.00 95.10 8 A 1 ATOM 63 O OG1 . THR A 1 8 ? 4.188 0.257 5.469 1.00 92.45 8 A 1 ATOM 64 C CG2 . THR A 1 8 ? 5.247 -1.832 4.963 1.00 91.78 8 A 1 ATOM 65 N N . LEU A 1 9 ? 3.204 -1.728 1.644 1.00 96.27 9 A 1 ATOM 66 C CA . LEU A 1 9 ? 2.986 -2.827 0.713 1.00 96.00 9 A 1 ATOM 67 C C . LEU A 1 9 ? 2.595 -2.296 -0.662 1.00 96.60 9 A 1 ATOM 68 O O . LEU A 1 9 ? 1.924 -2.980 -1.431 1.00 95.54 9 A 1 ATOM 69 C CB . LEU A 1 9 ? 1.885 -3.742 1.250 1.00 95.24 9 A 1 ATOM 70 C CG . LEU A 1 9 ? 1.985 -4.048 2.735 1.00 93.42 9 A 1 ATOM 71 C CD1 . LEU A 1 9 ? 0.806 -4.900 3.168 1.00 90.76 9 A 1 ATOM 72 C CD2 . LEU A 1 9 ? 3.294 -4.762 3.038 1.00 89.42 9 A 1 ATOM 73 N N . LEU A 1 10 ? 3.010 -1.081 -0.969 1.00 96.71 10 A 1 ATOM 74 C CA . LEU A 1 10 ? 2.654 -0.425 -2.220 1.00 96.06 10 A 1 ATOM 75 C C . LEU A 1 10 ? 2.957 -1.308 -3.424 1.00 96.38 10 A 1 ATOM 76 O O . LEU A 1 10 ? 2.213 -1.328 -4.399 1.00 94.88 10 A 1 ATOM 77 C CB . LEU A 1 10 ? 3.400 0.906 -2.336 1.00 94.99 10 A 1 ATOM 78 C CG . LEU A 1 10 ? 4.917 0.789 -2.167 1.00 93.63 10 A 1 ATOM 79 C CD1 . LEU A 1 10 ? 5.582 0.446 -3.489 1.00 90.16 10 A 1 ATOM 80 C CD2 . LEU A 1 10 ? 5.487 2.081 -1.624 1.00 88.62 10 A 1 ATOM 81 N N . GLY A 1 11 ? 4.053 -2.037 -3.359 1.00 95.45 11 A 1 ATOM 82 C CA . GLY A 1 11 ? 4.438 -2.908 -4.456 1.00 95.24 11 A 1 ATOM 83 C C . GLY A 1 11 ? 3.811 -4.281 -4.363 1.00 95.84 11 A 1 ATOM 84 O O . GLY A 1 11 ? 3.916 -5.079 -5.292 1.00 94.07 11 A 1 ATOM 85 N N . LEU A 1 12 ? 3.156 -4.554 -3.252 1.00 93.96 12 A 1 ATOM 86 C CA . LEU A 1 12 ? 2.539 -5.852 -3.017 1.00 94.47 12 A 1 ATOM 87 C C . LEU A 1 12 ? 1.039 -5.794 -3.238 1.00 95.14 12 A 1 ATOM 88 O O . LEU A 1 12 ? 0.507 -6.461 -4.122 1.00 92.09 12 A 1 ATOM 89 C CB . LEU A 1 12 ? 2.836 -6.316 -1.589 1.00 93.82 12 A 1 ATOM 90 C CG . LEU A 1 12 ? 4.317 -6.280 -1.224 1.00 91.82 12 A 1 ATOM 91 C CD1 . LEU A 1 12 ? 4.515 -6.772 0.196 1.00 88.00 12 A 1 ATOM 92 C CD2 . LEU A 1 12 ? 5.119 -7.121 -2.199 1.00 85.96 12 A 1 ATOM 93 N N . VAL A 1 13 ? 0.366 -5.008 -2.429 1.00 94.40 13 A 1 ATOM 94 C CA . VAL A 1 13 ? -1.085 -4.887 -2.531 1.00 93.21 13 A 1 ATOM 95 C C . VAL A 1 13 ? -1.585 -3.605 -1.897 1.00 92.17 13 A 1 ATOM 96 O O . VAL A 1 13 ? -1.715 -3.513 -0.680 1.00 88.63 13 A 1 ATOM 97 C CB . VAL A 1 13 ? -1.775 -6.082 -1.861 1.00 91.83 13 A 1 ATOM 98 C CG1 . VAL A 1 13 ? -1.289 -6.249 -0.423 1.00 86.31 13 A 1 ATOM 99 C CG2 . VAL A 1 13 ? -3.278 -5.923 -1.902 1.00 87.55 13 A 1 ATOM 100 N N . CYS A 1 14 ? -1.870 -2.628 -2.726 1.00 92.33 14 A 1 ATOM 101 C CA . CYS A 1 14 ? -2.404 -1.360 -2.237 1.00 92.04 14 A 1 ATOM 102 C C . CYS A 1 14 ? -3.758 -1.073 -2.861 1.00 91.23 14 A 1 ATOM 103 O O . CYS A 1 14 ? -3.839 -0.741 -4.044 1.00 86.84 14 A 1 ATOM 104 C CB . CYS A 1 14 ? -1.445 -0.222 -2.562 1.00 90.78 14 A 1 ATOM 105 S SG . CYS A 1 14 ? -2.122 1.397 -2.155 1.00 90.02 14 A 1 ATOM 106 N N . GLY A 1 15 ? -4.794 -1.175 -2.074 1.00 83.11 15 A 1 ATOM 107 C CA . GLY A 1 15 ? -6.141 -0.908 -2.562 1.00 79.10 15 A 1 ATOM 108 C C . GLY A 1 15 ? -7.176 -1.441 -1.613 1.00 76.11 15 A 1 ATOM 109 O O . GLY A 1 15 ? -8.227 -0.796 -1.445 1.00 71.91 15 A 1 ATOM 110 O OXT . GLY A 1 15 ? -6.943 -2.474 -1.010 1.00 72.48 15 A 1 #