# 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_spkb25807 # _entry.id spkb25807 # 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" "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" "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 ALA 4 1 n LEU 5 1 n VAL 6 1 n VAL 7 1 n LEU 8 1 n ALA 9 1 n LEU 10 1 n PHE 11 1 n GLY 12 1 n VAL 13 1 n SER 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 @ 2025-07-04 00:02:23)" _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 94.54 _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 86.47 1 1 A LYS 2 2 90.98 1 2 A VAL 3 2 96.83 1 3 A ALA 4 2 98.10 1 4 A LEU 5 2 96.04 1 5 A VAL 6 2 97.65 1 6 A VAL 7 2 97.38 1 7 A LEU 8 2 95.64 1 8 A ALA 9 2 97.51 1 9 A LEU 10 2 95.71 1 10 A PHE 11 2 93.94 1 11 A GLY 12 2 97.38 1 12 A VAL 13 2 96.18 1 13 A SER 14 2 95.83 1 14 A LEU 15 2 93.21 1 15 A ALA 16 2 88.39 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 ALA . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n VAL . 6 A 6 A 7 1 n VAL . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n ALA . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n PHE . 11 A 11 A 12 1 n GLY . 12 A 12 A 13 1 n VAL . 13 A 13 A 14 1 n SER . 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 ? -0.311 13.613 2.757 1.00 92.78 1 A 1 ATOM 2 C CA . MET A 1 1 ? 0.285 12.266 2.832 1.00 92.68 1 A 1 ATOM 3 C C . MET A 1 1 ? -0.791 11.192 2.730 1.00 93.25 1 A 1 ATOM 4 O O . MET A 1 1 ? -1.901 11.379 3.210 1.00 89.76 1 A 1 ATOM 5 C CB . MET A 1 1 ? 1.034 12.100 4.152 1.00 88.18 1 A 1 ATOM 6 C CG . MET A 1 1 ? 2.221 13.038 4.269 1.00 84.44 1 A 1 ATOM 7 S SD . MET A 1 1 ? 3.047 12.868 5.847 1.00 80.63 1 A 1 ATOM 8 C CE . MET A 1 1 ? 4.379 14.038 5.645 1.00 70.05 1 A 1 ATOM 9 N N . LYS A 1 2 ? -0.454 10.073 2.095 1.00 95.93 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -1.398 8.980 1.926 1.00 96.75 2 A 1 ATOM 11 C C . LYS A 1 2 ? -0.700 7.637 2.125 1.00 97.23 2 A 1 ATOM 12 O O . LYS A 1 2 ? -0.496 6.883 1.171 1.00 96.51 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -2.023 9.056 0.537 1.00 95.37 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -3.524 8.888 0.560 1.00 90.33 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -4.217 10.237 0.612 1.00 87.73 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -5.717 10.086 0.513 1.00 82.56 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -6.378 11.406 0.345 1.00 76.39 2 A 1 ATOM 18 N N . VAL A 1 3 ? -0.341 7.348 3.354 1.00 97.64 3 A 1 ATOM 19 C CA . VAL A 1 3 ? 0.340 6.098 3.692 1.00 98.06 3 A 1 ATOM 20 C C . VAL A 1 3 ? -0.567 4.897 3.443 1.00 98.25 3 A 1 ATOM 21 O O . VAL A 1 3 ? -0.103 3.810 3.091 1.00 97.76 3 A 1 ATOM 22 C CB . VAL A 1 3 ? 0.800 6.108 5.156 1.00 97.45 3 A 1 ATOM 23 C CG1 . VAL A 1 3 ? 1.599 4.860 5.474 1.00 94.15 3 A 1 ATOM 24 C CG2 . VAL A 1 3 ? 1.625 7.350 5.446 1.00 94.50 3 A 1 ATOM 25 N N . ALA A 1 4 ? -1.861 5.103 3.625 1.00 98.00 4 A 1 ATOM 26 C CA . ALA A 1 4 ? -2.842 4.038 3.426 1.00 98.22 4 A 1 ATOM 27 C C . ALA A 1 4 ? -2.827 3.526 1.989 1.00 98.36 4 A 1 ATOM 28 O O . ALA A 1 4 ? -2.954 2.327 1.743 1.00 97.98 4 A 1 ATOM 29 C CB . ALA A 1 4 ? -4.228 4.552 3.790 1.00 97.95 4 A 1 ATOM 30 N N . LEU A 1 5 ? -2.667 4.444 1.039 1.00 98.18 5 A 1 ATOM 31 C CA . LEU A 1 5 ? -2.628 4.088 -0.376 1.00 98.20 5 A 1 ATOM 32 C C . LEU A 1 5 ? -1.347 3.339 -0.718 1.00 98.29 5 A 1 ATOM 33 O O . LEU A 1 5 ? -1.365 2.369 -1.478 1.00 98.04 5 A 1 ATOM 34 C CB . LEU A 1 5 ? -2.740 5.351 -1.227 1.00 97.95 5 A 1 ATOM 35 C CG . LEU A 1 5 ? -4.123 5.569 -1.832 1.00 93.99 5 A 1 ATOM 36 C CD1 . LEU A 1 5 ? -4.292 7.009 -2.284 1.00 91.46 5 A 1 ATOM 37 C CD2 . LEU A 1 5 ? -4.322 4.621 -3.007 1.00 92.24 5 A 1 ATOM 38 N N . VAL A 1 6 ? -0.238 3.795 -0.154 1.00 98.20 6 A 1 ATOM 39 C CA . VAL A 1 6 ? 1.063 3.168 -0.387 1.00 98.23 6 A 1 ATOM 40 C C . VAL A 1 6 ? 1.085 1.753 0.175 1.00 98.31 6 A 1 ATOM 41 O O . VAL A 1 6 ? 1.601 0.827 -0.455 1.00 98.08 6 A 1 ATOM 42 C CB . VAL A 1 6 ? 2.195 3.995 0.251 1.00 97.97 6 A 1 ATOM 43 C CG1 . VAL A 1 6 ? 3.545 3.339 0.014 1.00 96.61 6 A 1 ATOM 44 C CG2 . VAL A 1 6 ? 2.193 5.410 -0.309 1.00 96.15 6 A 1 ATOM 45 N N . VAL A 1 7 ? 0.534 1.595 1.354 1.00 97.97 7 A 1 ATOM 46 C CA . VAL A 1 7 ? 0.490 0.292 2.014 1.00 97.96 7 A 1 ATOM 47 C C . VAL A 1 7 ? -0.384 -0.673 1.221 1.00 98.01 7 A 1 ATOM 48 O O . VAL A 1 7 ? -0.069 -1.858 1.092 1.00 97.78 7 A 1 ATOM 49 C CB . VAL A 1 7 ? -0.046 0.425 3.450 1.00 97.68 7 A 1 ATOM 50 C CG1 . VAL A 1 7 ? -0.218 -0.944 4.094 1.00 96.36 7 A 1 ATOM 51 C CG2 . VAL A 1 7 ? 0.902 1.272 4.288 1.00 95.87 7 A 1 ATOM 52 N N . LEU A 1 8 ? -1.478 -0.158 0.687 1.00 97.96 8 A 1 ATOM 53 C CA . LEU A 1 8 ? -2.406 -0.967 -0.096 1.00 97.69 8 A 1 ATOM 54 C C . LEU A 1 8 ? -1.720 -1.518 -1.340 1.00 97.91 8 A 1 ATOM 55 O O . LEU A 1 8 ? -1.924 -2.676 -1.708 1.00 97.71 8 A 1 ATOM 56 C CB . LEU A 1 8 ? -3.612 -0.121 -0.503 1.00 97.22 8 A 1 ATOM 57 C CG . LEU A 1 8 ? -4.732 -0.920 -1.159 1.00 92.71 8 A 1 ATOM 58 C CD1 . LEU A 1 8 ? -5.515 -1.691 -0.112 1.00 91.49 8 A 1 ATOM 59 C CD2 . LEU A 1 8 ? -5.658 0.003 -1.935 1.00 92.40 8 A 1 ATOM 60 N N . ALA A 1 9 ? -0.913 -0.687 -1.977 1.00 97.66 9 A 1 ATOM 61 C CA . ALA A 1 9 ? -0.187 -1.088 -3.176 1.00 97.57 9 A 1 ATOM 62 C C . ALA A 1 9 ? 0.815 -2.193 -2.861 1.00 97.86 9 A 1 ATOM 63 O O . ALA A 1 9 ? 0.973 -3.140 -3.629 1.00 97.29 9 A 1 ATOM 64 C CB . ALA A 1 9 ? 0.529 0.120 -3.771 1.00 97.18 9 A 1 ATOM 65 N N . LEU A 1 10 ? 1.484 -2.064 -1.721 1.00 97.78 10 A 1 ATOM 66 C CA . LEU A 1 10 ? 2.467 -3.057 -1.291 1.00 97.73 10 A 1 ATOM 67 C C . LEU A 1 10 ? 1.798 -4.385 -0.973 1.00 97.87 10 A 1 ATOM 68 O O . LEU A 1 10 ? 2.315 -5.453 -1.312 1.00 97.33 10 A 1 ATOM 69 C CB . LEU A 1 10 ? 3.214 -2.537 -0.061 1.00 97.35 10 A 1 ATOM 70 C CG . LEU A 1 10 ? 4.662 -2.148 -0.339 1.00 94.42 10 A 1 ATOM 71 C CD1 . LEU A 1 10 ? 5.134 -1.088 0.642 1.00 91.73 10 A 1 ATOM 72 C CD2 . LEU A 1 10 ? 5.557 -3.370 -0.268 1.00 91.50 10 A 1 ATOM 73 N N . PHE A 1 11 ? 0.653 -4.315 -0.322 1.00 97.43 11 A 1 ATOM 74 C CA . PHE A 1 11 ? -0.100 -5.513 0.029 1.00 97.10 11 A 1 ATOM 75 C C . PHE A 1 11 ? -0.593 -6.232 -1.213 1.00 97.45 11 A 1 ATOM 76 O O . PHE A 1 11 ? -0.585 -7.460 -1.279 1.00 96.44 11 A 1 ATOM 77 C CB . PHE A 1 11 ? -1.284 -5.132 0.915 1.00 96.45 11 A 1 ATOM 78 C CG . PHE A 1 11 ? -1.136 -5.643 2.325 1.00 94.26 11 A 1 ATOM 79 C CD1 . PHE A 1 11 ? -0.294 -5.009 3.219 1.00 91.03 11 A 1 ATOM 80 C CD2 . PHE A 1 11 ? -1.842 -6.762 2.736 1.00 91.51 11 A 1 ATOM 81 C CE1 . PHE A 1 11 ? -0.148 -5.480 4.516 1.00 90.59 11 A 1 ATOM 82 C CE2 . PHE A 1 11 ? -1.705 -7.241 4.034 1.00 90.18 11 A 1 ATOM 83 C CZ . PHE A 1 11 ? -0.857 -6.599 4.928 1.00 90.93 11 A 1 ATOM 84 N N . GLY A 1 12 ? -1.022 -5.458 -2.198 1.00 97.39 12 A 1 ATOM 85 C CA . GLY A 1 12 ? -1.507 -6.027 -3.448 1.00 97.39 12 A 1 ATOM 86 C C . GLY A 1 12 ? -0.412 -6.720 -4.228 1.00 97.69 12 A 1 ATOM 87 O O . GLY A 1 12 ? -0.634 -7.760 -4.848 1.00 97.05 12 A 1 ATOM 88 N N . VAL A 1 13 ? 0.787 -6.164 -4.203 1.00 97.76 13 A 1 ATOM 89 C CA . VAL A 1 13 ? 1.940 -6.738 -4.900 1.00 97.55 13 A 1 ATOM 90 C C . VAL A 1 13 ? 2.341 -8.068 -4.279 1.00 97.72 13 A 1 ATOM 91 O O . VAL A 1 13 ? 2.696 -9.014 -4.988 1.00 96.66 13 A 1 ATOM 92 C CB . VAL A 1 13 ? 3.138 -5.772 -4.862 1.00 96.65 13 A 1 ATOM 93 C CG1 . VAL A 1 13 ? 4.367 -6.421 -5.475 1.00 93.52 13 A 1 ATOM 94 C CG2 . VAL A 1 13 ? 2.802 -4.491 -5.598 1.00 93.43 13 A 1 ATOM 95 N N . SER A 1 14 ? 2.288 -8.138 -2.961 1.00 97.31 14 A 1 ATOM 96 C CA . SER A 1 14 ? 2.659 -9.350 -2.236 1.00 97.42 14 A 1 ATOM 97 C C . SER A 1 14 ? 1.512 -10.359 -2.203 1.00 97.62 14 A 1 ATOM 98 O O . SER A 1 14 ? 1.659 -11.465 -1.683 1.00 96.71 14 A 1 ATOM 99 C CB . SER A 1 14 ? 3.082 -9.005 -0.810 1.00 96.52 14 A 1 ATOM 100 O OG . SER A 1 14 ? 4.368 -9.509 -0.533 1.00 89.40 14 A 1 ATOM 101 N N . LEU A 1 15 ? 0.375 -9.967 -2.751 1.00 96.27 15 A 1 ATOM 102 C CA . LEU A 1 15 ? -0.810 -10.818 -2.769 1.00 96.18 15 A 1 ATOM 103 C C . LEU A 1 15 ? -0.678 -11.920 -3.810 1.00 96.46 15 A 1 ATOM 104 O O . LEU A 1 15 ? -0.724 -13.113 -3.485 1.00 95.19 15 A 1 ATOM 105 C CB . LEU A 1 15 ? -2.055 -9.972 -3.042 1.00 94.93 15 A 1 ATOM 106 C CG . LEU A 1 15 ? -3.314 -10.452 -2.321 1.00 91.84 15 A 1 ATOM 107 C CD1 . LEU A 1 15 ? -4.375 -9.366 -2.347 1.00 88.72 15 A 1 ATOM 108 C CD2 . LEU A 1 15 ? -3.845 -11.726 -2.943 1.00 86.07 15 A 1 ATOM 109 N N . ALA A 1 16 ? -0.521 -11.533 -5.062 1.00 93.98 16 A 1 ATOM 110 C CA . ALA A 1 16 ? -0.400 -12.485 -6.165 1.00 92.61 16 A 1 ATOM 111 C C . ALA A 1 16 ? 1.054 -12.883 -6.364 1.00 90.95 16 A 1 ATOM 112 O O . ALA A 1 16 ? 1.329 -14.082 -6.571 1.00 85.76 16 A 1 ATOM 113 C CB . ALA A 1 16 ? -0.974 -11.880 -7.441 1.00 87.75 16 A 1 ATOM 114 O OXT . ALA A 1 16 ? 1.906 -11.996 -6.320 1.00 79.27 16 A 1 #