# 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_spkb19973 # _entry.id spkb19973 # 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" "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" "C9 H11 N O2" 165.189 PHE y PHENYLALANINE c1ccc(cc1)C[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" "C3 H7 N O3" 105.093 SER y SERINE C([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 LYS 2 1 n LEU 3 1 n SER 4 1 n LEU 5 1 n LEU 6 1 n ALA 7 1 n SER 8 1 n VAL 9 1 n ALA 10 1 n LEU 11 1 n VAL 12 1 n PRO 13 1 n PHE 14 1 n VAL 15 1 n SER 16 1 n ALA 17 # _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 @ 2025-07-08 14:56:49)" _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 87.99 _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 79.17 1 1 A LYS 2 2 82.46 1 2 A LEU 3 2 84.74 1 3 A SER 4 2 89.91 1 4 A LEU 5 2 88.49 1 5 A LEU 6 2 87.79 1 6 A ALA 7 2 90.25 1 7 A SER 8 2 90.76 1 8 A VAL 9 2 90.62 1 9 A ALA 10 2 92.50 1 10 A LEU 11 2 90.12 1 11 A VAL 12 2 90.54 1 12 A PRO 13 2 92.27 1 13 A PHE 14 2 88.30 1 14 A VAL 15 2 90.02 1 15 A SER 16 2 89.35 1 16 A ALA 17 2 83.58 1 17 # _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 LYS . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n SER . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n SER . 8 A 8 A 9 1 n VAL . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n VAL . 12 A 12 A 13 1 n PRO . 13 A 13 A 14 1 n PHE . 14 A 14 A 15 1 n VAL . 15 A 15 A 16 1 n SER . 16 A 16 A 17 1 n ALA . 17 A 17 # _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 ? -5.151 5.963 11.956 1.00 83.40 1 A 1 ATOM 2 C CA . MET A 1 1 ? -4.011 6.706 11.388 1.00 86.08 1 A 1 ATOM 3 C C . MET A 1 1 ? -3.069 5.763 10.638 1.00 87.33 1 A 1 ATOM 4 O O . MET A 1 1 ? -2.611 6.076 9.545 1.00 84.78 1 A 1 ATOM 5 C CB . MET A 1 1 ? -3.240 7.426 12.502 1.00 79.70 1 A 1 ATOM 6 C CG . MET A 1 1 ? -4.085 8.495 13.182 1.00 76.73 1 A 1 ATOM 7 S SD . MET A 1 1 ? -3.205 9.340 14.503 1.00 72.31 1 A 1 ATOM 8 C CE . MET A 1 1 ? -4.477 10.456 15.065 1.00 63.04 1 A 1 ATOM 9 N N . LYS A 1 2 ? -2.800 4.610 11.229 1.00 88.23 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -1.914 3.632 10.597 1.00 89.44 2 A 1 ATOM 11 C C . LYS A 1 2 ? -2.571 2.999 9.375 1.00 89.43 2 A 1 ATOM 12 O O . LYS A 1 2 ? -1.885 2.509 8.480 1.00 89.22 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -1.522 2.549 11.604 1.00 86.22 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -2.679 1.624 11.956 1.00 80.82 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -2.267 0.596 12.990 1.00 78.29 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -3.345 -0.466 13.165 1.00 73.20 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -3.083 -1.631 12.309 1.00 67.25 2 A 1 ATOM 18 N N . LEU A 1 3 ? -3.876 3.019 9.316 1.00 87.50 3 A 1 ATOM 19 C CA . LEU A 1 3 ? -4.623 2.440 8.199 1.00 88.10 3 A 1 ATOM 20 C C . LEU A 1 3 ? -4.349 3.203 6.906 1.00 89.86 3 A 1 ATOM 21 O O . LEU A 1 3 ? -4.396 2.632 5.818 1.00 87.13 3 A 1 ATOM 22 C CB . LEU A 1 3 ? -6.123 2.456 8.508 1.00 86.15 3 A 1 ATOM 23 C CG . LEU A 1 3 ? -6.536 1.516 9.641 1.00 82.88 3 A 1 ATOM 24 C CD1 . LEU A 1 3 ? -8.003 1.732 9.987 1.00 79.45 3 A 1 ATOM 25 C CD2 . LEU A 1 3 ? -6.302 0.067 9.237 1.00 76.85 3 A 1 ATOM 26 N N . SER A 1 4 ? -4.056 4.471 7.014 1.00 91.27 4 A 1 ATOM 27 C CA . SER A 1 4 ? -3.772 5.306 5.847 1.00 91.64 4 A 1 ATOM 28 C C . SER A 1 4 ? -2.480 4.862 5.159 1.00 92.19 4 A 1 ATOM 29 O O . SER A 1 4 ? -2.390 4.859 3.933 1.00 91.38 4 A 1 ATOM 30 C CB . SER A 1 4 ? -3.660 6.774 6.261 1.00 90.34 4 A 1 ATOM 31 O OG . SER A 1 4 ? -4.880 7.232 6.822 1.00 82.63 4 A 1 ATOM 32 N N . LEU A 1 5 ? -1.478 4.461 5.941 1.00 91.50 5 A 1 ATOM 33 C CA . LEU A 1 5 ? -0.194 4.014 5.401 1.00 91.54 5 A 1 ATOM 34 C C . LEU A 1 5 ? -0.334 2.661 4.710 1.00 92.84 5 A 1 ATOM 35 O O . LEU A 1 5 ? 0.168 2.464 3.603 1.00 91.40 5 A 1 ATOM 36 C CB . LEU A 1 5 ? 0.844 3.924 6.523 1.00 90.67 5 A 1 ATOM 37 C CG . LEU A 1 5 ? 1.208 5.273 7.153 1.00 85.13 5 A 1 ATOM 38 C CD1 . LEU A 1 5 ? 2.109 5.059 8.363 1.00 82.72 5 A 1 ATOM 39 C CD2 . LEU A 1 5 ? 1.900 6.173 6.138 1.00 82.10 5 A 1 ATOM 40 N N . LEU A 1 6 ? -1.009 1.729 5.345 1.00 91.27 6 A 1 ATOM 41 C CA . LEU A 1 6 ? -1.204 0.395 4.782 1.00 90.88 6 A 1 ATOM 42 C C . LEU A 1 6 ? -2.085 0.443 3.537 1.00 92.02 6 A 1 ATOM 43 O O . LEU A 1 6 ? -1.852 -0.286 2.574 1.00 90.94 6 A 1 ATOM 44 C CB . LEU A 1 6 ? -1.836 -0.518 5.833 1.00 89.51 6 A 1 ATOM 45 C CG . LEU A 1 6 ? -0.915 -0.847 7.005 1.00 84.04 6 A 1 ATOM 46 C CD1 . LEU A 1 6 ? -1.690 -1.594 8.084 1.00 82.55 6 A 1 ATOM 47 C CD2 . LEU A 1 6 ? 0.267 -1.682 6.535 1.00 81.14 6 A 1 ATOM 48 N N . ALA A 1 7 ? -3.086 1.286 3.554 1.00 90.33 7 A 1 ATOM 49 C CA . ALA A 1 7 ? -4.003 1.422 2.423 1.00 90.17 7 A 1 ATOM 50 C C . ALA A 1 7 ? -3.290 1.978 1.190 1.00 91.82 7 A 1 ATOM 51 O O . ALA A 1 7 ? -3.549 1.546 0.067 1.00 89.97 7 A 1 ATOM 52 C CB . ALA A 1 7 ? -5.166 2.329 2.812 1.00 88.95 7 A 1 ATOM 53 N N . SER A 1 8 ? -2.391 2.917 1.385 1.00 92.56 8 A 1 ATOM 54 C CA . SER A 1 8 ? -1.654 3.535 0.285 1.00 92.92 8 A 1 ATOM 55 C C . SER A 1 8 ? -0.610 2.583 -0.293 1.00 93.65 8 A 1 ATOM 56 O O . SER A 1 8 ? -0.457 2.477 -1.507 1.00 91.49 8 A 1 ATOM 57 C CB . SER A 1 8 ? -0.975 4.816 0.768 1.00 91.23 8 A 1 ATOM 58 O OG . SER A 1 8 ? -1.941 5.771 1.168 1.00 82.70 8 A 1 ATOM 59 N N . VAL A 1 9 ? 0.108 1.884 0.576 1.00 92.22 9 A 1 ATOM 60 C CA . VAL A 1 9 ? 1.149 0.944 0.153 1.00 91.86 9 A 1 ATOM 61 C C . VAL A 1 9 ? 0.546 -0.278 -0.540 1.00 93.36 9 A 1 ATOM 62 O O . VAL A 1 9 ? 1.175 -0.882 -1.411 1.00 92.03 9 A 1 ATOM 63 C CB . VAL A 1 9 ? 1.997 0.496 1.360 1.00 90.53 9 A 1 ATOM 64 C CG1 . VAL A 1 9 ? 3.016 -0.562 0.949 1.00 87.14 9 A 1 ATOM 65 C CG2 . VAL A 1 9 ? 2.720 1.692 1.963 1.00 87.19 9 A 1 ATOM 66 N N . ALA A 1 10 ? -0.654 -0.644 -0.158 1.00 92.81 10 A 1 ATOM 67 C CA . ALA A 1 10 ? -1.323 -1.814 -0.724 1.00 92.72 10 A 1 ATOM 68 C C . ALA A 1 10 ? -1.807 -1.570 -2.155 1.00 93.94 10 A 1 ATOM 69 O O . ALA A 1 10 ? -2.137 -2.512 -2.872 1.00 91.71 10 A 1 ATOM 70 C CB . ALA A 1 10 ? -2.500 -2.214 0.165 1.00 91.31 10 A 1 ATOM 71 N N . LEU A 1 11 ? -1.842 -0.330 -2.588 1.00 93.33 11 A 1 ATOM 72 C CA . LEU A 1 11 ? -2.319 0.009 -3.927 1.00 93.26 11 A 1 ATOM 73 C C . LEU A 1 11 ? -1.262 -0.261 -4.994 1.00 94.33 11 A 1 ATOM 74 O O . LEU A 1 11 ? -1.587 -0.711 -6.093 1.00 92.22 11 A 1 ATOM 75 C CB . LEU A 1 11 ? -2.733 1.483 -3.972 1.00 92.29 11 A 1 ATOM 76 C CG . LEU A 1 11 ? -3.948 1.819 -3.103 1.00 87.48 11 A 1 ATOM 77 C CD1 . LEU A 1 11 ? -4.174 3.324 -3.081 1.00 84.23 11 A 1 ATOM 78 C CD2 . LEU A 1 11 ? -5.187 1.111 -3.624 1.00 83.81 11 A 1 ATOM 79 N N . VAL A 1 12 ? -0.002 0.005 -4.678 1.00 93.08 12 A 1 ATOM 80 C CA . VAL A 1 12 ? 1.098 -0.192 -5.627 1.00 92.28 12 A 1 ATOM 81 C C . VAL A 1 12 ? 1.289 -1.662 -6.018 1.00 93.11 12 A 1 ATOM 82 O O . VAL A 1 12 ? 1.307 -1.981 -7.212 1.00 91.04 12 A 1 ATOM 83 C CB . VAL A 1 12 ? 2.411 0.379 -5.062 1.00 90.44 12 A 1 ATOM 84 C CG1 . VAL A 1 12 ? 3.560 0.149 -6.036 1.00 85.82 12 A 1 ATOM 85 C CG2 . VAL A 1 12 ? 2.256 1.861 -4.773 1.00 87.98 12 A 1 ATOM 86 N N . PRO A 1 13 ? 1.462 -2.569 -5.042 1.00 93.64 13 A 1 ATOM 87 C CA . PRO A 1 13 ? 1.691 -3.987 -5.349 1.00 92.97 13 A 1 ATOM 88 C C . PRO A 1 13 ? 0.483 -4.670 -5.987 1.00 93.66 13 A 1 ATOM 89 O O . PRO A 1 13 ? 0.640 -5.509 -6.873 1.00 91.79 13 A 1 ATOM 90 C CB . PRO A 1 13 ? 2.013 -4.609 -3.983 1.00 91.06 13 A 1 ATOM 91 C CG . PRO A 1 13 ? 1.355 -3.708 -3.000 1.00 89.76 13 A 1 ATOM 92 C CD . PRO A 1 13 ? 1.456 -2.325 -3.597 1.00 93.03 13 A 1 ATOM 93 N N . PHE A 1 14 ? -0.707 -4.336 -5.557 1.00 91.50 14 A 1 ATOM 94 C CA . PHE A 1 14 ? -1.916 -4.961 -6.087 1.00 91.51 14 A 1 ATOM 95 C C . PHE A 1 14 ? -2.188 -4.535 -7.527 1.00 93.10 14 A 1 ATOM 96 O O . PHE A 1 14 ? -2.646 -5.336 -8.342 1.00 90.87 14 A 1 ATOM 97 C CB . PHE A 1 14 ? -3.115 -4.617 -5.200 1.00 90.63 14 A 1 ATOM 98 C CG . PHE A 1 14 ? -3.192 -5.486 -3.967 1.00 87.19 14 A 1 ATOM 99 C CD1 . PHE A 1 14 ? -3.756 -6.750 -4.035 1.00 85.62 14 A 1 ATOM 100 C CD2 . PHE A 1 14 ? -2.693 -5.038 -2.754 1.00 86.15 14 A 1 ATOM 101 C CE1 . PHE A 1 14 ? -3.826 -7.558 -2.906 1.00 84.92 14 A 1 ATOM 102 C CE2 . PHE A 1 14 ? -2.757 -5.844 -1.619 1.00 84.66 14 A 1 ATOM 103 C CZ . PHE A 1 14 ? -3.326 -7.104 -1.698 1.00 85.19 14 A 1 ATOM 104 N N . VAL A 1 15 ? -1.907 -3.294 -7.851 1.00 92.84 15 A 1 ATOM 105 C CA . VAL A 1 15 ? -2.133 -2.798 -9.210 1.00 91.83 15 A 1 ATOM 106 C C . VAL A 1 15 ? -1.075 -3.323 -10.177 1.00 92.79 15 A 1 ATOM 107 O O . VAL A 1 15 ? -1.321 -3.421 -11.380 1.00 91.31 15 A 1 ATOM 108 C CB . VAL A 1 15 ? -2.128 -1.258 -9.239 1.00 90.02 15 A 1 ATOM 109 C CG1 . VAL A 1 15 ? -0.714 -0.724 -9.034 1.00 85.15 15 A 1 ATOM 110 C CG2 . VAL A 1 15 ? -2.689 -0.761 -10.558 1.00 86.22 15 A 1 ATOM 111 N N . SER A 1 16 ? 0.098 -3.664 -9.668 1.00 92.23 16 A 1 ATOM 112 C CA . SER A 1 16 ? 1.197 -4.178 -10.487 1.00 92.01 16 A 1 ATOM 113 C C . SER A 1 16 ? 0.925 -5.601 -10.972 1.00 91.56 16 A 1 ATOM 114 O O . SER A 1 16 ? 1.462 -6.032 -11.995 1.00 89.72 16 A 1 ATOM 115 C CB . SER A 1 16 ? 2.500 -4.155 -9.690 1.00 90.22 16 A 1 ATOM 116 O OG . SER A 1 16 ? 3.581 -4.569 -10.493 1.00 80.35 16 A 1 ATOM 117 N N . ALA A 1 17 ? 0.099 -6.345 -10.250 1.00 89.77 17 A 1 ATOM 118 C CA . ALA A 1 17 ? -0.232 -7.719 -10.591 1.00 87.29 17 A 1 ATOM 119 C C . ALA A 1 17 ? -1.160 -7.783 -11.809 1.00 84.75 17 A 1 ATOM 120 O O . ALA A 1 17 ? -1.693 -6.738 -12.222 1.00 81.99 17 A 1 ATOM 121 C CB . ALA A 1 17 ? -0.861 -8.410 -9.386 1.00 82.69 17 A 1 ATOM 122 O OXT . ALA A 1 17 ? -1.380 -8.886 -12.347 1.00 74.98 17 A 1 #