# 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_spkb39023 # _entry.id spkb39023 # 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" "C4 H9 N O3" 119.119 THR y THREONINE C[C@H]([C@@H](C(=O)O)N)O ? "L-PEPTIDE LINKING" "C9 H11 N O3" 181.189 TYR y TYROSINE c1cc(ccc1C[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 LYS 3 1 n THR 4 1 n MET 5 1 n LEU 6 1 n ALA 7 1 n ILE 8 1 n ILE 9 1 n LEU 10 1 n ILE 11 1 n PRO 12 1 n LEU 13 1 n VAL 14 1 n TYR 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 17:44:56)" _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 94.55 _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 89.84 1 1 A LYS 2 2 88.20 1 2 A LYS 3 2 90.83 1 3 A THR 4 2 95.73 1 4 A MET 5 2 93.21 1 5 A LEU 6 2 95.46 1 6 A ALA 7 2 97.90 1 7 A ILE 8 2 96.88 1 8 A ILE 9 2 96.35 1 9 A LEU 10 2 95.81 1 10 A ILE 11 2 96.35 1 11 A PRO 12 2 97.80 1 12 A LEU 13 2 95.78 1 13 A VAL 14 2 96.85 1 14 A TYR 15 2 94.89 1 15 A ALA 16 2 94.00 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 LYS . 3 A 3 A 4 1 n THR . 4 A 4 A 5 1 n MET . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n ILE . 8 A 8 A 9 1 n ILE . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n ILE . 11 A 11 A 12 1 n PRO . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n TYR . 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 ? -10.966 1.995 5.151 1.00 94.15 1 A 1 ATOM 2 C CA . MET A 1 1 ? -10.760 2.796 3.930 1.00 95.43 1 A 1 ATOM 3 C C . MET A 1 1 ? -9.813 2.088 2.965 1.00 95.77 1 A 1 ATOM 4 O O . MET A 1 1 ? -8.865 1.442 3.385 1.00 94.40 1 A 1 ATOM 5 C CB . MET A 1 1 ? -10.176 4.160 4.282 1.00 92.53 1 A 1 ATOM 6 C CG . MET A 1 1 ? -11.063 4.961 5.212 1.00 87.24 1 A 1 ATOM 7 S SD . MET A 1 1 ? -10.350 6.550 5.637 1.00 83.77 1 A 1 ATOM 8 C CE . MET A 1 1 ? -11.581 7.166 6.761 1.00 75.44 1 A 1 ATOM 9 N N . LYS A 1 2 ? -10.068 2.224 1.675 1.00 95.16 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -9.236 1.591 0.655 1.00 95.98 2 A 1 ATOM 11 C C . LYS A 1 2 ? -7.921 2.344 0.467 1.00 96.49 2 A 1 ATOM 12 O O . LYS A 1 2 ? -6.857 1.740 0.349 1.00 95.64 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -9.990 1.527 -0.674 1.00 94.80 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -11.223 0.636 -0.629 1.00 86.80 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -11.935 0.613 -1.966 1.00 84.37 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -13.175 -0.258 -1.914 1.00 75.99 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -13.898 -0.263 -3.216 1.00 68.55 2 A 1 ATOM 18 N N . LYS A 1 3 ? -8.001 3.665 0.431 1.00 96.25 3 A 1 ATOM 19 C CA . LYS A 1 3 ? -6.822 4.507 0.255 1.00 96.99 3 A 1 ATOM 20 C C . LYS A 1 3 ? -5.862 4.351 1.425 1.00 97.26 3 A 1 ATOM 21 O O . LYS A 1 3 ? -4.644 4.343 1.245 1.00 96.42 3 A 1 ATOM 22 C CB . LYS A 1 3 ? -7.236 5.966 0.111 1.00 96.14 3 A 1 ATOM 23 C CG . LYS A 1 3 ? -8.100 6.243 -1.115 1.00 91.11 3 A 1 ATOM 24 C CD . LYS A 1 3 ? -7.323 6.020 -2.401 1.00 87.59 3 A 1 ATOM 25 C CE . LYS A 1 3 ? -8.149 6.343 -3.628 1.00 81.56 3 A 1 ATOM 26 N NZ . LYS A 1 3 ? -7.381 6.140 -4.882 1.00 74.11 3 A 1 ATOM 27 N N . THR A 1 4 ? -6.416 4.232 2.615 1.00 97.31 4 A 1 ATOM 28 C CA . THR A 1 4 ? -5.612 4.090 3.823 1.00 97.50 4 A 1 ATOM 29 C C . THR A 1 4 ? -4.855 2.768 3.819 1.00 97.68 4 A 1 ATOM 30 O O . THR A 1 4 ? -3.696 2.702 4.236 1.00 97.05 4 A 1 ATOM 31 C CB . THR A 1 4 ? -6.487 4.159 5.080 1.00 97.07 4 A 1 ATOM 32 O OG1 . THR A 1 4 ? -7.271 5.356 5.060 1.00 92.64 4 A 1 ATOM 33 C CG2 . THR A 1 4 ? -5.627 4.145 6.335 1.00 90.87 4 A 1 ATOM 34 N N . MET A 1 5 ? -5.506 1.722 3.343 1.00 96.97 5 A 1 ATOM 35 C CA . MET A 1 5 ? -4.899 0.401 3.301 1.00 97.22 5 A 1 ATOM 36 C C . MET A 1 5 ? -3.719 0.374 2.335 1.00 97.65 5 A 1 ATOM 37 O O . MET A 1 5 ? -2.737 -0.327 2.560 1.00 97.34 5 A 1 ATOM 38 C CB . MET A 1 5 ? -5.934 -0.642 2.892 1.00 96.86 5 A 1 ATOM 39 C CG . MET A 1 5 ? -5.490 -2.056 3.173 1.00 92.87 5 A 1 ATOM 40 S SD . MET A 1 5 ? -6.786 -3.260 2.870 1.00 87.58 5 A 1 ATOM 41 C CE . MET A 1 5 ? -5.958 -4.747 3.413 1.00 79.18 5 A 1 ATOM 42 N N . LEU A 1 6 ? -3.813 1.141 1.271 1.00 97.74 6 A 1 ATOM 43 C CA . LEU A 1 6 ? -2.751 1.221 0.279 1.00 97.71 6 A 1 ATOM 44 C C . LEU A 1 6 ? -1.619 2.116 0.760 1.00 98.00 6 A 1 ATOM 45 O O . LEU A 1 6 ? -0.462 1.926 0.385 1.00 97.95 6 A 1 ATOM 46 C CB . LEU A 1 6 ? -3.304 1.762 -1.038 1.00 97.43 6 A 1 ATOM 47 C CG . LEU A 1 6 ? -4.221 0.807 -1.786 1.00 93.24 6 A 1 ATOM 48 C CD1 . LEU A 1 6 ? -4.920 1.521 -2.925 1.00 90.39 6 A 1 ATOM 49 C CD2 . LEU A 1 6 ? -3.432 -0.378 -2.316 1.00 91.22 6 A 1 ATOM 50 N N . ALA A 1 7 ? -1.964 3.088 1.579 1.00 97.85 7 A 1 ATOM 51 C CA . ALA A 1 7 ? -0.986 4.034 2.104 1.00 97.95 7 A 1 ATOM 52 C C . ALA A 1 7 ? -0.004 3.366 3.057 1.00 98.20 7 A 1 ATOM 53 O O . ALA A 1 7 ? 1.159 3.755 3.137 1.00 97.90 7 A 1 ATOM 54 C CB . ALA A 1 7 ? -1.697 5.179 2.814 1.00 97.61 7 A 1 ATOM 55 N N . ILE A 1 8 ? -0.475 2.355 3.770 1.00 97.89 8 A 1 ATOM 56 C CA . ILE A 1 8 ? 0.359 1.658 4.739 1.00 97.80 8 A 1 ATOM 57 C C . ILE A 1 8 ? 1.301 0.661 4.070 1.00 97.96 8 A 1 ATOM 58 O O . ILE A 1 8 ? 2.293 0.240 4.662 1.00 97.48 8 A 1 ATOM 59 C CB . ILE A 1 8 ? -0.504 0.921 5.785 1.00 97.54 8 A 1 ATOM 60 C CG1 . ILE A 1 8 ? -1.408 -0.103 5.112 1.00 96.15 8 A 1 ATOM 61 C CG2 . ILE A 1 8 ? -1.321 1.916 6.589 1.00 96.06 8 A 1 ATOM 62 C CD1 . ILE A 1 8 ? -2.170 -0.983 6.084 1.00 94.19 8 A 1 ATOM 63 N N . ILE A 1 9 ? 0.992 0.285 2.845 1.00 97.66 9 A 1 ATOM 64 C CA . ILE A 1 9 ? 1.809 -0.669 2.111 1.00 97.43 9 A 1 ATOM 65 C C . ILE A 1 9 ? 2.720 0.013 1.098 1.00 97.73 9 A 1 ATOM 66 O O . ILE A 1 9 ? 3.753 -0.536 0.718 1.00 97.24 9 A 1 ATOM 67 C CB . ILE A 1 9 ? 0.932 -1.711 1.385 1.00 97.14 9 A 1 ATOM 68 C CG1 . ILE A 1 9 ? 0.022 -1.041 0.362 1.00 95.48 9 A 1 ATOM 69 C CG2 . ILE A 1 9 ? 0.117 -2.502 2.394 1.00 95.40 9 A 1 ATOM 70 C CD1 . ILE A 1 9 ? -0.763 -2.019 -0.491 1.00 92.72 9 A 1 ATOM 71 N N . LEU A 1 10 ? 2.336 1.191 0.656 1.00 97.96 10 A 1 ATOM 72 C CA . LEU A 1 10 ? 3.123 1.921 -0.330 1.00 97.87 10 A 1 ATOM 73 C C . LEU A 1 10 ? 4.273 2.678 0.321 1.00 97.99 10 A 1 ATOM 74 O O . LEU A 1 10 ? 5.326 2.878 -0.292 1.00 97.65 10 A 1 ATOM 75 C CB . LEU A 1 10 ? 2.229 2.890 -1.118 1.00 97.47 10 A 1 ATOM 76 C CG . LEU A 1 10 ? 1.605 4.022 -0.308 1.00 94.44 10 A 1 ATOM 77 C CD1 . LEU A 1 10 ? 2.533 5.229 -0.263 1.00 91.00 10 A 1 ATOM 78 C CD2 . LEU A 1 10 ? 0.271 4.426 -0.922 1.00 92.08 10 A 1 ATOM 79 N N . ILE A 1 11 ? 4.085 3.107 1.566 1.00 97.98 11 A 1 ATOM 80 C CA . ILE A 1 11 ? 5.117 3.841 2.292 1.00 97.80 11 A 1 ATOM 81 C C . ILE A 1 11 ? 6.362 2.982 2.519 1.00 98.04 11 A 1 ATOM 82 O O . ILE A 1 11 ? 7.476 3.393 2.175 1.00 97.62 11 A 1 ATOM 83 C CB . ILE A 1 11 ? 4.583 4.363 3.640 1.00 97.16 11 A 1 ATOM 84 C CG1 . ILE A 1 11 ? 3.496 5.409 3.422 1.00 94.58 11 A 1 ATOM 85 C CG2 . ILE A 1 11 ? 5.730 4.967 4.448 1.00 94.98 11 A 1 ATOM 86 C CD1 . ILE A 1 11 ? 2.773 5.799 4.697 1.00 92.67 11 A 1 ATOM 87 N N . PRO A 1 12 ? 6.197 1.801 3.124 1.00 98.27 12 A 1 ATOM 88 C CA . PRO A 1 12 ? 7.340 0.918 3.373 1.00 98.06 12 A 1 ATOM 89 C C . PRO A 1 12 ? 7.967 0.408 2.086 1.00 98.20 12 A 1 ATOM 90 O O . PRO A 1 12 ? 9.165 0.123 2.051 1.00 97.65 12 A 1 ATOM 91 C CB . PRO A 1 12 ? 6.725 -0.238 4.171 1.00 97.54 12 A 1 ATOM 92 C CG . PRO A 1 12 ? 5.286 -0.226 3.805 1.00 96.89 12 A 1 ATOM 93 C CD . PRO A 1 12 ? 4.944 1.225 3.606 1.00 98.01 12 A 1 ATOM 94 N N . LEU A 1 13 ? 7.184 0.289 1.045 1.00 97.95 13 A 1 ATOM 95 C CA . LEU A 1 13 ? 7.665 -0.182 -0.249 1.00 97.91 13 A 1 ATOM 96 C C . LEU A 1 13 ? 8.686 0.784 -0.832 1.00 98.11 13 A 1 ATOM 97 O O . LEU A 1 13 ? 9.687 0.366 -1.416 1.00 97.52 13 A 1 ATOM 98 C CB . LEU A 1 13 ? 6.494 -0.341 -1.220 1.00 97.53 13 A 1 ATOM 99 C CG . LEU A 1 13 ? 6.857 -0.981 -2.555 1.00 94.41 13 A 1 ATOM 100 C CD1 . LEU A 1 13 ? 7.340 -2.411 -2.344 1.00 91.01 13 A 1 ATOM 101 C CD2 . LEU A 1 13 ? 5.666 -0.965 -3.497 1.00 91.84 13 A 1 ATOM 102 N N . VAL A 1 14 ? 8.436 2.067 -0.675 1.00 98.05 14 A 1 ATOM 103 C CA . VAL A 1 14 ? 9.337 3.100 -1.172 1.00 98.00 14 A 1 ATOM 104 C C . VAL A 1 14 ? 10.539 3.268 -0.255 1.00 98.14 14 A 1 ATOM 105 O O . VAL A 1 14 ? 11.653 3.538 -0.712 1.00 97.48 14 A 1 ATOM 106 C CB . VAL A 1 14 ? 8.613 4.451 -1.305 1.00 97.37 14 A 1 ATOM 107 C CG1 . VAL A 1 14 ? 9.570 5.525 -1.801 1.00 94.60 14 A 1 ATOM 108 C CG2 . VAL A 1 14 ? 7.429 4.325 -2.241 1.00 94.33 14 A 1 ATOM 109 N N . TYR A 1 15 ? 10.300 3.115 1.041 1.00 98.16 15 A 1 ATOM 110 C CA . TYR A 1 15 ? 11.357 3.259 2.026 1.00 97.99 15 A 1 ATOM 111 C C . TYR A 1 15 ? 12.282 2.048 2.015 1.00 98.02 15 A 1 ATOM 112 O O . TYR A 1 15 ? 13.476 2.172 2.298 1.00 97.27 15 A 1 ATOM 113 C CB . TYR A 1 15 ? 10.755 3.436 3.425 1.00 97.40 15 A 1 ATOM 114 C CG . TYR A 1 15 ? 10.297 4.852 3.704 1.00 95.68 15 A 1 ATOM 115 C CD1 . TYR A 1 15 ? 9.277 5.434 2.970 1.00 93.34 15 A 1 ATOM 116 C CD2 . TYR A 1 15 ? 10.895 5.602 4.707 1.00 93.13 15 A 1 ATOM 117 C CE1 . TYR A 1 15 ? 8.862 6.731 3.220 1.00 92.35 15 A 1 ATOM 118 C CE2 . TYR A 1 15 ? 10.484 6.902 4.974 1.00 91.95 15 A 1 ATOM 119 C CZ . TYR A 1 15 ? 9.466 7.459 4.222 1.00 92.43 15 A 1 ATOM 120 O OH . TYR A 1 15 ? 9.057 8.744 4.476 1.00 90.92 15 A 1 ATOM 121 N N . ALA A 1 16 ? 11.736 0.897 1.692 1.00 97.08 16 A 1 ATOM 122 C CA . ALA A 1 16 ? 12.486 -0.350 1.659 1.00 96.43 16 A 1 ATOM 123 C C . ALA A 1 16 ? 13.501 -0.333 0.521 1.00 95.73 16 A 1 ATOM 124 O O . ALA A 1 16 ? 14.690 -0.606 0.785 1.00 93.14 16 A 1 ATOM 125 C CB . ALA A 1 16 ? 11.536 -1.534 1.515 1.00 94.84 16 A 1 ATOM 126 O OXT . ALA A 1 16 ? 13.111 -0.071 -0.613 1.00 86.77 16 A 1 #