# 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_spkb34344 # _entry.id spkb34344 # 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" "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" "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 LYS 2 1 n LEU 3 1 n SER 4 1 n THR 5 1 n PHE 6 1 n ILE 7 1 n ILE 8 1 n MET 9 1 n ILE 10 1 n SER 11 1 n LEU 12 1 n ALA 13 1 n VAL 14 1 n ALA 15 1 n LEU 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 @ 2025-07-13 16:10:11)" _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 95.57 _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 87.91 1 1 A LYS 2 2 90.95 1 2 A LEU 3 2 95.27 1 3 A SER 4 2 96.61 1 4 A THR 5 2 96.35 1 5 A PHE 6 2 96.30 1 6 A ILE 7 2 97.43 1 7 A ILE 8 2 97.24 1 8 A MET 9 2 93.90 1 9 A ILE 10 2 96.40 1 10 A SER 11 2 97.25 1 11 A LEU 12 2 96.89 1 12 A ALA 13 2 98.55 1 13 A VAL 14 2 97.99 1 14 A ALA 15 2 98.66 1 15 A LEU 16 2 96.19 1 16 A ALA 17 2 94.01 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 THR . 5 A 5 A 6 1 n PHE . 6 A 6 A 7 1 n ILE . 7 A 7 A 8 1 n ILE . 8 A 8 A 9 1 n MET . 9 A 9 A 10 1 n ILE . 10 A 10 A 11 1 n SER . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n LEU . 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 ? 1.800 11.149 0.408 1.00 92.94 1 A 1 ATOM 2 C CA . MET A 1 1 ? 1.047 9.928 0.746 1.00 94.49 1 A 1 ATOM 3 C C . MET A 1 1 ? 1.491 9.367 2.096 1.00 95.27 1 A 1 ATOM 4 O O . MET A 1 1 ? 2.677 9.328 2.399 1.00 92.88 1 A 1 ATOM 5 C CB . MET A 1 1 ? 1.238 8.859 -0.325 1.00 89.78 1 A 1 ATOM 6 C CG . MET A 1 1 ? 2.679 8.702 -0.761 1.00 84.11 1 A 1 ATOM 7 S SD . MET A 1 1 ? 2.812 7.777 -2.297 1.00 81.71 1 A 1 ATOM 8 C CE . MET A 1 1 ? 4.310 8.469 -2.960 1.00 72.10 1 A 1 ATOM 9 N N . LYS A 1 2 ? 0.542 8.945 2.909 1.00 96.08 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 0.819 8.392 4.229 1.00 96.88 2 A 1 ATOM 11 C C . LYS A 1 2 ? 1.414 6.990 4.138 1.00 97.50 2 A 1 ATOM 12 O O . LYS A 1 2 ? 1.296 6.319 3.114 1.00 97.18 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -0.468 8.349 5.048 1.00 95.36 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -0.811 9.687 5.680 1.00 90.06 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -2.087 9.592 6.485 1.00 87.89 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -2.425 10.918 7.140 1.00 81.91 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -1.856 11.009 8.503 1.00 75.69 2 A 1 ATOM 18 N N . LEU A 1 3 ? 2.041 6.558 5.231 1.00 97.37 3 A 1 ATOM 19 C CA . LEU A 1 3 ? 2.642 5.228 5.292 1.00 97.83 3 A 1 ATOM 20 C C . LEU A 1 3 ? 1.557 4.159 5.196 1.00 98.19 3 A 1 ATOM 21 O O . LEU A 1 3 ? 1.773 3.093 4.619 1.00 97.78 3 A 1 ATOM 22 C CB . LEU A 1 3 ? 3.429 5.090 6.597 1.00 97.43 3 A 1 ATOM 23 C CG . LEU A 1 3 ? 4.663 4.205 6.468 1.00 93.55 3 A 1 ATOM 24 C CD1 . LEU A 1 3 ? 5.659 4.546 7.574 1.00 90.07 3 A 1 ATOM 25 C CD2 . LEU A 1 3 ? 4.294 2.741 6.540 1.00 89.91 3 A 1 ATOM 26 N N . SER A 1 4 ? 0.383 4.458 5.747 1.00 98.39 4 A 1 ATOM 27 C CA . SER A 1 4 ? -0.745 3.528 5.711 1.00 98.50 4 A 1 ATOM 28 C C . SER A 1 4 ? -1.193 3.280 4.275 1.00 98.61 4 A 1 ATOM 29 O O . SER A 1 4 ? -1.587 2.171 3.923 1.00 98.28 4 A 1 ATOM 30 C CB . SER A 1 4 ? -1.905 4.088 6.527 1.00 98.11 4 A 1 ATOM 31 O OG . SER A 1 4 ? -2.248 5.374 6.070 1.00 87.74 4 A 1 ATOM 32 N N . THR A 1 5 ? -1.126 4.311 3.438 1.00 98.07 5 A 1 ATOM 33 C CA . THR A 1 5 ? -1.510 4.194 2.034 1.00 98.25 5 A 1 ATOM 34 C C . THR A 1 5 ? -0.546 3.260 1.305 1.00 98.39 5 A 1 ATOM 35 O O . THR A 1 5 ? -0.954 2.481 0.443 1.00 98.12 5 A 1 ATOM 36 C CB . THR A 1 5 ? -1.508 5.565 1.353 1.00 97.95 5 A 1 ATOM 37 O OG1 . THR A 1 5 ? -2.320 6.471 2.095 1.00 92.92 5 A 1 ATOM 38 C CG2 . THR A 1 5 ? -2.047 5.463 -0.065 1.00 90.76 5 A 1 ATOM 39 N N . PHE A 1 6 ? 0.736 3.343 1.648 1.00 98.39 6 A 1 ATOM 40 C CA . PHE A 1 6 ? 1.754 2.481 1.054 1.00 98.40 6 A 1 ATOM 41 C C . PHE A 1 6 ? 1.462 1.018 1.369 1.00 98.52 6 A 1 ATOM 42 O O . PHE A 1 6 ? 1.539 0.154 0.496 1.00 98.33 6 A 1 ATOM 43 C CB . PHE A 1 6 ? 3.138 2.852 1.595 1.00 98.20 6 A 1 ATOM 44 C CG . PHE A 1 6 ? 3.913 3.761 0.671 1.00 96.99 6 A 1 ATOM 45 C CD1 . PHE A 1 6 ? 4.187 3.368 -0.627 1.00 94.34 6 A 1 ATOM 46 C CD2 . PHE A 1 6 ? 4.382 4.988 1.118 1.00 94.67 6 A 1 ATOM 47 C CE1 . PHE A 1 6 ? 4.916 4.188 -1.478 1.00 93.89 6 A 1 ATOM 48 C CE2 . PHE A 1 6 ? 5.114 5.814 0.272 1.00 94.08 6 A 1 ATOM 49 C CZ . PHE A 1 6 ? 5.383 5.415 -1.027 1.00 93.48 6 A 1 ATOM 50 N N . ILE A 1 7 ? 1.133 0.748 2.621 1.00 98.43 7 A 1 ATOM 51 C CA . ILE A 1 7 ? 0.846 -0.615 3.062 1.00 98.49 7 A 1 ATOM 52 C C . ILE A 1 7 ? -0.348 -1.185 2.303 1.00 98.57 7 A 1 ATOM 53 O O . ILE A 1 7 ? -0.336 -2.348 1.890 1.00 98.48 7 A 1 ATOM 54 C CB . ILE A 1 7 ? 0.577 -0.646 4.575 1.00 98.42 7 A 1 ATOM 55 C CG1 . ILE A 1 7 ? 1.836 -0.204 5.336 1.00 97.22 7 A 1 ATOM 56 C CG2 . ILE A 1 7 ? 0.167 -2.053 5.020 1.00 97.02 7 A 1 ATOM 57 C CD1 . ILE A 1 7 ? 1.582 0.062 6.805 1.00 92.81 7 A 1 ATOM 58 N N . ILE A 1 8 ? -1.374 -0.367 2.115 1.00 98.43 8 A 1 ATOM 59 C CA . ILE A 1 8 ? -2.580 -0.806 1.413 1.00 98.41 8 A 1 ATOM 60 C C . ILE A 1 8 ? -2.261 -1.132 -0.045 1.00 98.46 8 A 1 ATOM 61 O O . ILE A 1 8 ? -2.712 -2.149 -0.578 1.00 98.35 8 A 1 ATOM 62 C CB . ILE A 1 8 ? -3.678 0.271 1.492 1.00 98.31 8 A 1 ATOM 63 C CG1 . ILE A 1 8 ? -4.136 0.448 2.945 1.00 97.06 8 A 1 ATOM 64 C CG2 . ILE A 1 8 ? -4.874 -0.113 0.615 1.00 96.72 8 A 1 ATOM 65 C CD1 . ILE A 1 8 ? -4.975 1.694 3.163 1.00 92.21 8 A 1 ATOM 66 N N . MET A 1 9 ? -1.489 -0.267 -0.699 1.00 98.24 9 A 1 ATOM 67 C CA . MET A 1 9 ? -1.119 -0.485 -2.099 1.00 98.30 9 A 1 ATOM 68 C C . MET A 1 9 ? -0.280 -1.749 -2.257 1.00 98.41 9 A 1 ATOM 69 O O . MET A 1 9 ? -0.478 -2.525 -3.190 1.00 98.38 9 A 1 ATOM 70 C CB . MET A 1 9 ? -0.344 0.718 -2.633 1.00 98.16 9 A 1 ATOM 71 C CG . MET A 1 9 ? -1.248 1.896 -2.950 1.00 93.96 9 A 1 ATOM 72 S SD . MET A 1 9 ? -0.397 3.191 -3.852 1.00 87.44 9 A 1 ATOM 73 C CE . MET A 1 9 ? -1.764 4.316 -4.132 1.00 78.30 9 A 1 ATOM 74 N N . ILE A 1 10 ? 0.657 -1.948 -1.338 1.00 97.97 10 A 1 ATOM 75 C CA . ILE A 1 10 ? 1.517 -3.127 -1.381 1.00 97.91 10 A 1 ATOM 76 C C . ILE A 1 10 ? 0.691 -4.388 -1.148 1.00 98.16 10 A 1 ATOM 77 O O . ILE A 1 10 ? 0.886 -5.401 -1.825 1.00 98.11 10 A 1 ATOM 78 C CB . ILE A 1 10 ? 2.640 -3.020 -0.330 1.00 97.51 10 A 1 ATOM 79 C CG1 . ILE A 1 10 ? 3.587 -1.861 -0.679 1.00 95.58 10 A 1 ATOM 80 C CG2 . ILE A 1 10 ? 3.434 -4.330 -0.268 1.00 95.12 10 A 1 ATOM 81 C CD1 . ILE A 1 10 ? 4.506 -1.478 0.462 1.00 90.87 10 A 1 ATOM 82 N N . SER A 1 11 ? -0.226 -4.330 -0.205 1.00 98.49 11 A 1 ATOM 83 C CA . SER A 1 11 ? -1.079 -5.474 0.110 1.00 98.54 11 A 1 ATOM 84 C C . SER A 1 11 ? -1.924 -5.874 -1.097 1.00 98.65 11 A 1 ATOM 85 O O . SER A 1 11 ? -2.080 -7.058 -1.390 1.00 98.49 11 A 1 ATOM 86 C CB . SER A 1 11 ? -1.988 -5.143 1.290 1.00 98.31 11 A 1 ATOM 87 O OG . SER A 1 11 ? -1.228 -4.919 2.459 1.00 91.05 11 A 1 ATOM 88 N N . LEU A 1 12 ? -2.457 -4.874 -1.800 1.00 98.61 12 A 1 ATOM 89 C CA . LEU A 1 12 ? -3.274 -5.129 -2.983 1.00 98.57 12 A 1 ATOM 90 C C . LEU A 1 12 ? -2.434 -5.740 -4.096 1.00 98.67 12 A 1 ATOM 91 O O . LEU A 1 12 ? -2.879 -6.656 -4.791 1.00 98.52 12 A 1 ATOM 92 C CB . LEU A 1 12 ? -3.907 -3.822 -3.464 1.00 98.30 12 A 1 ATOM 93 C CG . LEU A 1 12 ? -5.084 -3.351 -2.613 1.00 95.23 12 A 1 ATOM 94 C CD1 . LEU A 1 12 ? -5.441 -1.911 -2.945 1.00 93.03 12 A 1 ATOM 95 C CD2 . LEU A 1 12 ? -6.292 -4.251 -2.840 1.00 94.17 12 A 1 ATOM 96 N N . ALA A 1 13 ? -1.219 -5.230 -4.272 1.00 98.59 13 A 1 ATOM 97 C CA . ALA A 1 13 ? -0.319 -5.737 -5.302 1.00 98.62 13 A 1 ATOM 98 C C . ALA A 1 13 ? 0.044 -7.196 -5.041 1.00 98.71 13 A 1 ATOM 99 O O . ALA A 1 13 ? 0.086 -8.007 -5.965 1.00 98.49 13 A 1 ATOM 100 C CB . ALA A 1 13 ? 0.941 -4.879 -5.352 1.00 98.35 13 A 1 ATOM 101 N N . VAL A 1 14 ? 0.309 -7.531 -3.786 1.00 98.72 14 A 1 ATOM 102 C CA . VAL A 1 14 ? 0.663 -8.900 -3.410 1.00 98.69 14 A 1 ATOM 103 C C . VAL A 1 14 ? -0.525 -9.837 -3.590 1.00 98.74 14 A 1 ATOM 104 O O . VAL A 1 14 ? -0.369 -10.978 -4.035 1.00 98.44 14 A 1 ATOM 105 C CB . VAL A 1 14 ? 1.158 -8.949 -1.955 1.00 98.29 14 A 1 ATOM 106 C CG1 . VAL A 1 14 ? 1.410 -10.385 -1.519 1.00 96.27 14 A 1 ATOM 107 C CG2 . VAL A 1 14 ? 2.432 -8.137 -1.814 1.00 96.78 14 A 1 ATOM 108 N N . ALA A 1 15 ? -1.709 -9.360 -3.235 1.00 98.77 15 A 1 ATOM 109 C CA . ALA A 1 15 ? -2.923 -10.166 -3.349 1.00 98.75 15 A 1 ATOM 110 C C . ALA A 1 15 ? -3.266 -10.460 -4.807 1.00 98.78 15 A 1 ATOM 111 O O . ALA A 1 15 ? -3.725 -11.555 -5.134 1.00 98.48 15 A 1 ATOM 112 C CB . ALA A 1 15 ? -4.086 -9.444 -2.674 1.00 98.52 15 A 1 ATOM 113 N N . LEU A 1 16 ? -3.055 -9.479 -5.680 1.00 98.45 16 A 1 ATOM 114 C CA . LEU A 1 16 ? -3.349 -9.630 -7.102 1.00 98.36 16 A 1 ATOM 115 C C . LEU A 1 16 ? -2.248 -10.392 -7.828 1.00 98.43 16 A 1 ATOM 116 O O . LEU A 1 16 ? -2.492 -10.986 -8.882 1.00 97.85 16 A 1 ATOM 117 C CB . LEU A 1 16 ? -3.530 -8.249 -7.742 1.00 97.87 16 A 1 ATOM 118 C CG . LEU A 1 16 ? -4.783 -7.502 -7.283 1.00 95.43 16 A 1 ATOM 119 C CD1 . LEU A 1 16 ? -4.748 -6.056 -7.756 1.00 91.87 16 A 1 ATOM 120 C CD2 . LEU A 1 16 ? -6.033 -8.193 -7.816 1.00 91.27 16 A 1 ATOM 121 N N . ALA A 1 17 ? -1.042 -10.367 -7.272 1.00 97.58 17 A 1 ATOM 122 C CA . ALA A 1 17 ? 0.105 -11.043 -7.877 1.00 96.85 17 A 1 ATOM 123 C C . ALA A 1 17 ? -0.111 -12.555 -7.905 1.00 96.08 17 A 1 ATOM 124 O O . ALA A 1 17 ? 0.481 -13.228 -8.768 1.00 92.40 17 A 1 ATOM 125 C CB . ALA A 1 17 ? 1.381 -10.685 -7.114 1.00 94.86 17 A 1 ATOM 126 O OXT . ALA A 1 17 ? -0.858 -13.082 -7.087 1.00 86.27 17 A 1 #