# 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_spkb25019 # _entry.id spkb25019 # 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 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" "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 VAL 3 1 n SER 4 1 n SER 5 1 n ALA 6 1 n ILE 7 1 n ALA 8 1 n LEU 9 1 n LEU 10 1 n LEU 11 1 n PRO 12 1 n VAL 13 1 n VAL 14 1 n ALA 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 08:13:18)" _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 93.89 _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 84.36 1 1 A LYS 2 2 88.37 1 2 A VAL 3 2 92.32 1 3 A SER 4 2 94.19 1 4 A SER 5 2 94.83 1 5 A ALA 6 2 96.82 1 6 A ILE 7 2 94.59 1 7 A ALA 8 2 96.65 1 8 A LEU 9 2 94.69 1 9 A LEU 10 2 94.90 1 10 A LEU 11 2 94.21 1 11 A PRO 12 2 96.82 1 12 A VAL 13 2 96.30 1 13 A VAL 14 2 96.40 1 14 A ALA 15 2 97.56 1 15 A ALA 16 2 94.71 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 LYS . 2 A 2 A 3 1 n VAL . 3 A 3 A 4 1 n SER . 4 A 4 A 5 1 n SER . 5 A 5 A 6 1 n ALA . 6 A 6 A 7 1 n ILE . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n PRO . 12 A 12 A 13 1 n VAL . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n ALA . 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 ? 1.319 7.712 8.553 1.00 88.80 1 A 1 ATOM 2 C CA . MET A 1 1 ? 0.091 7.018 8.106 1.00 90.12 1 A 1 ATOM 3 C C . MET A 1 1 ? 0.345 5.517 7.957 1.00 91.41 1 A 1 ATOM 4 O O . MET A 1 1 ? 0.805 5.058 6.920 1.00 87.98 1 A 1 ATOM 5 C CB . MET A 1 1 ? -0.361 7.569 6.761 1.00 85.62 1 A 1 ATOM 6 C CG . MET A 1 1 ? -0.692 9.047 6.838 1.00 82.89 1 A 1 ATOM 7 S SD . MET A 1 1 ? -1.200 9.709 5.244 1.00 78.87 1 A 1 ATOM 8 C CE . MET A 1 1 ? -1.205 11.448 5.613 1.00 69.16 1 A 1 ATOM 9 N N . LYS A 1 2 ? 0.048 4.768 9.001 1.00 92.16 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 0.259 3.314 8.990 1.00 94.08 2 A 1 ATOM 11 C C . LYS A 1 2 ? -0.730 2.624 8.054 1.00 94.36 2 A 1 ATOM 12 O O . LYS A 1 2 ? -0.360 1.731 7.295 1.00 93.98 2 A 1 ATOM 13 C CB . LYS A 1 2 ? 0.101 2.758 10.407 1.00 92.60 2 A 1 ATOM 14 C CG . LYS A 1 2 ? 1.139 3.301 11.375 1.00 87.28 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 0.955 2.713 12.763 1.00 85.90 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 1.993 3.261 13.725 1.00 80.58 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 1.790 4.717 13.962 1.00 74.42 2 A 1 ATOM 18 N N . VAL A 1 3 ? -1.991 3.026 8.105 1.00 93.76 3 A 1 ATOM 19 C CA . VAL A 1 3 ? -3.034 2.437 7.264 1.00 94.40 3 A 1 ATOM 20 C C . VAL A 1 3 ? -2.785 2.738 5.791 1.00 95.05 3 A 1 ATOM 21 O O . VAL A 1 3 ? -2.885 1.856 4.934 1.00 93.79 3 A 1 ATOM 22 C CB . VAL A 1 3 ? -4.421 2.961 7.672 1.00 92.61 3 A 1 ATOM 23 C CG1 . VAL A 1 3 ? -5.498 2.325 6.806 1.00 87.96 3 A 1 ATOM 24 C CG2 . VAL A 1 3 ? -4.686 2.671 9.143 1.00 88.66 3 A 1 ATOM 25 N N . SER A 1 4 ? -2.473 3.977 5.495 1.00 95.94 4 A 1 ATOM 26 C CA . SER A 1 4 ? -2.216 4.402 4.118 1.00 95.96 4 A 1 ATOM 27 C C . SER A 1 4 ? -1.029 3.649 3.527 1.00 96.47 4 A 1 ATOM 28 O O . SER A 1 4 ? -1.016 3.308 2.346 1.00 95.99 4 A 1 ATOM 29 C CB . SER A 1 4 ? -1.949 5.906 4.077 1.00 94.80 4 A 1 ATOM 30 O OG . SER A 1 4 ? -1.757 6.327 2.746 1.00 85.98 4 A 1 ATOM 31 N N . SER A 1 5 ? -0.045 3.379 4.347 1.00 96.04 5 A 1 ATOM 32 C CA . SER A 1 5 ? 1.155 2.666 3.912 1.00 96.32 5 A 1 ATOM 33 C C . SER A 1 5 ? 0.817 1.243 3.478 1.00 97.00 5 A 1 ATOM 34 O O . SER A 1 5 ? 1.352 0.738 2.496 1.00 96.61 5 A 1 ATOM 35 C CB . SER A 1 5 ? 2.174 2.626 5.049 1.00 95.16 5 A 1 ATOM 36 O OG . SER A 1 5 ? 3.344 1.976 4.619 1.00 87.83 5 A 1 ATOM 37 N N . ALA A 1 6 ? -0.074 0.601 4.209 1.00 96.46 6 A 1 ATOM 38 C CA . ALA A 1 6 ? -0.478 -0.769 3.907 1.00 96.88 6 A 1 ATOM 39 C C . ALA A 1 6 ? -1.169 -0.852 2.549 1.00 97.50 6 A 1 ATOM 40 O O . ALA A 1 6 ? -0.976 -1.806 1.798 1.00 96.94 6 A 1 ATOM 41 C CB . ALA A 1 6 ? -1.415 -1.272 4.998 1.00 96.32 6 A 1 ATOM 42 N N . ILE A 1 7 ? -1.973 0.139 2.238 1.00 96.41 7 A 1 ATOM 43 C CA . ILE A 1 7 ? -2.699 0.184 0.971 1.00 96.26 7 A 1 ATOM 44 C C . ILE A 1 7 ? -1.729 0.355 -0.191 1.00 96.78 7 A 1 ATOM 45 O O . ILE A 1 7 ? -1.919 -0.213 -1.270 1.00 96.65 7 A 1 ATOM 46 C CB . ILE A 1 7 ? -3.717 1.333 0.973 1.00 96.11 7 A 1 ATOM 47 C CG1 . ILE A 1 7 ? -4.727 1.148 2.106 1.00 93.60 7 A 1 ATOM 48 C CG2 . ILE A 1 7 ? -4.452 1.380 -0.371 1.00 93.03 7 A 1 ATOM 49 C CD1 . ILE A 1 7 ? -5.559 2.399 2.350 1.00 87.92 7 A 1 ATOM 50 N N . ALA A 1 8 ? -0.700 1.134 0.029 1.00 96.73 8 A 1 ATOM 51 C CA . ALA A 1 8 ? 0.303 1.388 -1.001 1.00 96.69 8 A 1 ATOM 52 C C . ALA A 1 8 ? 1.070 0.114 -1.347 1.00 97.28 8 A 1 ATOM 53 O O . ALA A 1 8 ? 1.578 -0.037 -2.454 1.00 96.50 8 A 1 ATOM 54 C CB . ALA A 1 8 ? 1.263 2.468 -0.518 1.00 96.05 8 A 1 ATOM 55 N N . LEU A 1 9 ? 1.158 -0.802 -0.399 1.00 96.47 9 A 1 ATOM 56 C CA . LEU A 1 9 ? 1.869 -2.061 -0.603 1.00 96.24 9 A 1 ATOM 57 C C . LEU A 1 9 ? 1.013 -3.065 -1.369 1.00 96.93 9 A 1 ATOM 58 O O . LEU A 1 9 ? 1.533 -3.919 -2.085 1.00 95.88 9 A 1 ATOM 59 C CB . LEU A 1 9 ? 2.270 -2.648 0.751 1.00 95.76 9 A 1 ATOM 60 C CG . LEU A 1 9 ? 3.661 -2.226 1.213 1.00 93.08 9 A 1 ATOM 61 C CD1 . LEU A 1 9 ? 3.681 -0.744 1.571 1.00 91.60 9 A 1 ATOM 62 C CD2 . LEU A 1 9 ? 4.107 -3.058 2.410 1.00 91.57 9 A 1 ATOM 63 N N . LEU A 1 10 ? -0.293 -2.960 -1.214 1.00 96.31 10 A 1 ATOM 64 C CA . LEU A 1 10 ? -1.218 -3.881 -1.868 1.00 96.32 10 A 1 ATOM 65 C C . LEU A 1 10 ? -1.333 -3.587 -3.358 1.00 96.97 10 A 1 ATOM 66 O O . LEU A 1 10 ? -1.466 -4.506 -4.168 1.00 96.19 10 A 1 ATOM 67 C CB . LEU A 1 10 ? -2.598 -3.763 -1.213 1.00 96.01 10 A 1 ATOM 68 C CG . LEU A 1 10 ? -2.656 -4.355 0.194 1.00 93.80 10 A 1 ATOM 69 C CD1 . LEU A 1 10 ? -3.889 -3.849 0.930 1.00 91.94 10 A 1 ATOM 70 C CD2 . LEU A 1 10 ? -2.678 -5.878 0.126 1.00 91.66 10 A 1 ATOM 71 N N . LEU A 1 11 ? -1.291 -2.322 -3.718 1.00 96.47 11 A 1 ATOM 72 C CA . LEU A 1 11 ? -1.411 -1.908 -5.117 1.00 96.45 11 A 1 ATOM 73 C C . LEU A 1 11 ? -0.288 -2.478 -5.987 1.00 97.16 11 A 1 ATOM 74 O O . LEU A 1 11 ? -0.560 -3.103 -7.016 1.00 96.56 11 A 1 ATOM 75 C CB . LEU A 1 11 ? -1.423 -0.377 -5.202 1.00 95.50 11 A 1 ATOM 76 C CG . LEU A 1 11 ? -1.748 0.147 -6.596 1.00 92.17 11 A 1 ATOM 77 C CD1 . LEU A 1 11 ? -3.213 -0.107 -6.928 1.00 90.14 11 A 1 ATOM 78 C CD2 . LEU A 1 11 ? -1.449 1.642 -6.680 1.00 89.23 11 A 1 ATOM 79 N N . PRO A 1 12 ? 0.967 -2.262 -5.611 1.00 97.31 12 A 1 ATOM 80 C CA . PRO A 1 12 ? 2.104 -2.751 -6.399 1.00 97.13 12 A 1 ATOM 81 C C . PRO A 1 12 ? 2.163 -4.270 -6.459 1.00 97.61 12 A 1 ATOM 82 O O . PRO A 1 12 ? 2.576 -4.840 -7.469 1.00 96.90 12 A 1 ATOM 83 C CB . PRO A 1 12 ? 3.323 -2.184 -5.662 1.00 96.30 12 A 1 ATOM 84 C CG . PRO A 1 12 ? 2.848 -1.953 -4.267 1.00 95.64 12 A 1 ATOM 85 C CD . PRO A 1 12 ? 1.396 -1.556 -4.407 1.00 96.86 12 A 1 ATOM 86 N N . VAL A 1 13 ? 1.763 -4.934 -5.403 1.00 97.09 13 A 1 ATOM 87 C CA . VAL A 1 13 ? 1.778 -6.394 -5.347 1.00 97.23 13 A 1 ATOM 88 C C . VAL A 1 13 ? 0.772 -6.981 -6.332 1.00 97.71 13 A 1 ATOM 89 O O . VAL A 1 13 ? 1.044 -7.986 -6.994 1.00 97.10 13 A 1 ATOM 90 C CB . VAL A 1 13 ? 1.460 -6.887 -3.924 1.00 96.52 13 A 1 ATOM 91 C CG1 . VAL A 1 13 ? 1.359 -8.406 -3.897 1.00 94.28 13 A 1 ATOM 92 C CG2 . VAL A 1 13 ? 2.540 -6.424 -2.957 1.00 94.17 13 A 1 ATOM 93 N N . VAL A 1 14 ? -0.388 -6.369 -6.417 1.00 97.49 14 A 1 ATOM 94 C CA . VAL A 1 14 ? -1.441 -6.833 -7.320 1.00 97.40 14 A 1 ATOM 95 C C . VAL A 1 14 ? -1.062 -6.582 -8.774 1.00 97.77 14 A 1 ATOM 96 O O . VAL A 1 14 ? -1.363 -7.394 -9.654 1.00 97.43 14 A 1 ATOM 97 C CB . VAL A 1 14 ? -2.772 -6.127 -7.011 1.00 96.62 14 A 1 ATOM 98 C CG1 . VAL A 1 14 ? -3.841 -6.534 -8.019 1.00 94.03 14 A 1 ATOM 99 C CG2 . VAL A 1 14 ? -3.226 -6.469 -5.603 1.00 94.03 14 A 1 ATOM 100 N N . ALA A 1 15 ? -0.433 -5.465 -9.031 1.00 97.87 15 A 1 ATOM 101 C CA . ALA A 1 15 ? -0.018 -5.088 -10.381 1.00 97.70 15 A 1 ATOM 102 C C . ALA A 1 15 ? 1.093 -5.994 -10.902 1.00 97.90 15 A 1 ATOM 103 O O . ALA A 1 15 ? 1.264 -6.151 -12.109 1.00 97.40 15 A 1 ATOM 104 C CB . ALA A 1 15 ? 0.446 -3.635 -10.392 1.00 96.91 15 A 1 ATOM 105 N N . ALA A 1 16 ? 1.862 -6.586 -10.003 1.00 97.37 16 A 1 ATOM 106 C CA . ALA A 1 16 ? 2.976 -7.446 -10.373 1.00 96.75 16 A 1 ATOM 107 C C . ALA A 1 16 ? 2.510 -8.641 -11.193 1.00 96.10 16 A 1 ATOM 108 O O . ALA A 1 16 ? 1.476 -9.235 -10.851 1.00 94.02 16 A 1 ATOM 109 C CB . ALA A 1 16 ? 3.713 -7.905 -9.121 1.00 95.27 16 A 1 ATOM 110 O OXT . ALA A 1 16 ? 3.192 -8.996 -12.157 1.00 88.73 16 A 1 #