# 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_spkb28784 # _entry.id spkb28784 # 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 H10 N3 O2" 156.162 HIS y HISTIDINE c1c([nH+]c[nH]1)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 HIS 3 1 n SER 4 1 n VAL 5 1 n LEU 6 1 n ALA 7 1 n GLY 8 1 n LEU 9 1 n PHE 10 1 n ALA 11 1 n THR 12 1 n GLY 13 1 n ALA 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 @ 2025-07-12 08:22:40)" _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 91.37 _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 84.15 1 1 A LYS 2 2 84.99 1 2 A HIS 3 2 88.54 1 3 A SER 4 2 91.86 1 4 A VAL 5 2 94.82 1 5 A LEU 6 2 92.80 1 6 A ALA 7 2 96.31 1 7 A GLY 8 2 96.12 1 8 A LEU 9 2 93.97 1 9 A PHE 10 2 92.54 1 10 A ALA 11 2 96.40 1 11 A THR 12 2 94.32 1 12 A GLY 13 2 95.38 1 13 A ALA 14 2 94.57 1 14 A LEU 15 2 90.16 1 15 A ALA 16 2 84.67 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 HIS . 3 A 3 A 4 1 n SER . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n GLY . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n PHE . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n THR . 12 A 12 A 13 1 n GLY . 13 A 13 A 14 1 n ALA . 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 ? 5.120 -9.299 0.976 1.00 88.50 1 A 1 ATOM 2 C CA . MET A 1 1 ? 4.655 -8.824 2.286 1.00 90.30 1 A 1 ATOM 3 C C . MET A 1 1 ? 3.240 -8.260 2.182 1.00 91.06 1 A 1 ATOM 4 O O . MET A 1 1 ? 2.895 -7.628 1.186 1.00 87.78 1 A 1 ATOM 5 C CB . MET A 1 1 ? 5.580 -7.736 2.827 1.00 85.72 1 A 1 ATOM 6 C CG . MET A 1 1 ? 6.981 -8.254 3.094 1.00 82.71 1 A 1 ATOM 7 S SD . MET A 1 1 ? 8.067 -6.962 3.712 1.00 78.75 1 A 1 ATOM 8 C CE . MET A 1 1 ? 9.541 -7.910 4.007 1.00 68.40 1 A 1 ATOM 9 N N . LYS A 1 2 ? 2.450 -8.487 3.217 1.00 89.22 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 1.066 -8.004 3.243 1.00 91.10 2 A 1 ATOM 11 C C . LYS A 1 2 ? 1.008 -6.482 3.327 1.00 91.67 2 A 1 ATOM 12 O O . LYS A 1 2 ? 0.196 -5.839 2.667 1.00 91.17 2 A 1 ATOM 13 C CB . LYS A 1 2 ? 0.330 -8.609 4.441 1.00 88.52 2 A 1 ATOM 14 C CG . LYS A 1 2 ? 0.203 -10.116 4.372 1.00 83.81 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -0.578 -10.644 5.559 1.00 82.80 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -0.767 -12.150 5.463 1.00 75.91 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 0.523 -12.873 5.592 1.00 70.72 2 A 1 ATOM 18 N N . HIS A 1 3 ? 1.873 -5.914 4.144 1.00 93.05 3 A 1 ATOM 19 C CA . HIS A 1 3 ? 1.909 -4.470 4.351 1.00 93.88 3 A 1 ATOM 20 C C . HIS A 1 3 ? 2.371 -3.732 3.098 1.00 95.04 3 A 1 ATOM 21 O O . HIS A 1 3 ? 1.966 -2.593 2.852 1.00 93.17 3 A 1 ATOM 22 C CB . HIS A 1 3 ? 2.839 -4.143 5.515 1.00 92.36 3 A 1 ATOM 23 C CG . HIS A 1 3 ? 2.476 -4.875 6.772 1.00 89.88 3 A 1 ATOM 24 N ND1 . HIS A 1 3 ? 3.139 -5.987 7.219 1.00 81.25 3 A 1 ATOM 25 C CD2 . HIS A 1 3 ? 1.495 -4.638 7.672 1.00 80.27 3 A 1 ATOM 26 C CE1 . HIS A 1 3 ? 2.578 -6.396 8.346 1.00 82.76 3 A 1 ATOM 27 N NE2 . HIS A 1 3 ? 1.575 -5.599 8.650 1.00 83.76 3 A 1 ATOM 28 N N . SER A 1 4 ? 3.199 -4.377 2.304 1.00 93.43 4 A 1 ATOM 29 C CA . SER A 1 4 ? 3.715 -3.777 1.076 1.00 94.18 4 A 1 ATOM 30 C C . SER A 1 4 ? 2.591 -3.492 0.087 1.00 95.36 4 A 1 ATOM 31 O O . SER A 1 4 ? 2.568 -2.447 -0.561 1.00 93.51 4 A 1 ATOM 32 C CB . SER A 1 4 ? 4.746 -4.693 0.426 1.00 92.10 4 A 1 ATOM 33 O OG . SER A 1 4 ? 5.298 -4.083 -0.709 1.00 82.56 4 A 1 ATOM 34 N N . VAL A 1 5 ? 1.638 -4.415 -0.009 1.00 94.30 5 A 1 ATOM 35 C CA . VAL A 1 5 ? 0.496 -4.260 -0.907 1.00 95.71 5 A 1 ATOM 36 C C . VAL A 1 5 ? -0.365 -3.080 -0.474 1.00 96.29 5 A 1 ATOM 37 O O . VAL A 1 5 ? -0.809 -2.280 -1.298 1.00 95.39 5 A 1 ATOM 38 C CB . VAL A 1 5 ? -0.354 -5.539 -0.938 1.00 95.49 5 A 1 ATOM 39 C CG1 . VAL A 1 5 ? -1.568 -5.356 -1.831 1.00 93.52 5 A 1 ATOM 40 C CG2 . VAL A 1 5 ? 0.481 -6.716 -1.414 1.00 93.06 5 A 1 ATOM 41 N N . LEU A 1 6 ? -0.589 -2.979 0.819 1.00 95.12 6 A 1 ATOM 42 C CA . LEU A 1 6 ? -1.390 -1.893 1.367 1.00 95.06 6 A 1 ATOM 43 C C . LEU A 1 6 ? -0.714 -0.551 1.134 1.00 95.43 6 A 1 ATOM 44 O O . LEU A 1 6 ? -1.370 0.436 0.799 1.00 95.34 6 A 1 ATOM 45 C CB . LEU A 1 6 ? -1.609 -2.109 2.862 1.00 94.71 6 A 1 ATOM 46 C CG . LEU A 1 6 ? -2.513 -1.074 3.514 1.00 90.65 6 A 1 ATOM 47 C CD1 . LEU A 1 6 ? -3.916 -1.145 2.941 1.00 88.33 6 A 1 ATOM 48 C CD2 . LEU A 1 6 ? -2.541 -1.280 5.020 1.00 87.72 6 A 1 ATOM 49 N N . ALA A 1 7 ? 0.592 -0.515 1.317 1.00 96.41 7 A 1 ATOM 50 C CA . ALA A 1 7 ? 1.366 0.705 1.119 1.00 96.48 7 A 1 ATOM 51 C C . ALA A 1 7 ? 1.291 1.176 -0.328 1.00 96.85 7 A 1 ATOM 52 O O . ALA A 1 7 ? 1.117 2.366 -0.594 1.00 96.02 7 A 1 ATOM 53 C CB . ALA A 1 7 ? 2.818 0.466 1.519 1.00 95.81 7 A 1 ATOM 54 N N . GLY A 1 8 ? 1.411 0.240 -1.258 1.00 95.86 8 A 1 ATOM 55 C CA . GLY A 1 8 ? 1.340 0.566 -2.676 1.00 95.75 8 A 1 ATOM 56 C C . GLY A 1 8 ? -0.037 1.057 -3.074 1.00 96.65 8 A 1 ATOM 57 O O . GLY A 1 8 ? -0.174 2.022 -3.825 1.00 96.22 8 A 1 ATOM 58 N N . LEU A 1 9 ? -1.068 0.395 -2.555 1.00 95.00 9 A 1 ATOM 59 C CA . LEU A 1 9 ? -2.447 0.772 -2.844 1.00 95.38 9 A 1 ATOM 60 C C . LEU A 1 9 ? -2.759 2.152 -2.285 1.00 96.47 9 A 1 ATOM 61 O O . LEU A 1 9 ? -3.427 2.958 -2.931 1.00 96.10 9 A 1 ATOM 62 C CB . LEU A 1 9 ? -3.405 -0.257 -2.246 1.00 94.99 9 A 1 ATOM 63 C CG . LEU A 1 9 ? -4.875 0.008 -2.558 1.00 92.97 9 A 1 ATOM 64 C CD1 . LEU A 1 9 ? -5.135 -0.083 -4.051 1.00 90.58 9 A 1 ATOM 65 C CD2 . LEU A 1 9 ? -5.762 -0.975 -1.807 1.00 90.30 9 A 1 ATOM 66 N N . PHE A 1 10 ? -2.273 2.414 -1.086 1.00 94.64 10 A 1 ATOM 67 C CA . PHE A 1 10 ? -2.485 3.703 -0.444 1.00 94.86 10 A 1 ATOM 68 C C . PHE A 1 10 ? -1.816 4.816 -1.231 1.00 95.98 10 A 1 ATOM 69 O O . PHE A 1 10 ? -2.394 5.888 -1.425 1.00 95.39 10 A 1 ATOM 70 C CB . PHE A 1 10 ? -1.939 3.680 0.980 1.00 94.19 10 A 1 ATOM 71 C CG . PHE A 1 10 ? -2.152 4.975 1.712 1.00 92.96 10 A 1 ATOM 72 C CD1 . PHE A 1 10 ? -3.395 5.295 2.231 1.00 90.00 10 A 1 ATOM 73 C CD2 . PHE A 1 10 ? -1.108 5.871 1.873 1.00 90.54 10 A 1 ATOM 74 C CE1 . PHE A 1 10 ? -3.599 6.488 2.902 1.00 89.90 10 A 1 ATOM 75 C CE2 . PHE A 1 10 ? -1.303 7.074 2.540 1.00 89.48 10 A 1 ATOM 76 C CZ . PHE A 1 10 ? -2.552 7.382 3.057 1.00 90.03 10 A 1 ATOM 77 N N . ALA A 1 11 ? -0.604 4.564 -1.684 1.00 96.46 11 A 1 ATOM 78 C CA . ALA A 1 11 ? 0.142 5.548 -2.457 1.00 96.59 11 A 1 ATOM 79 C C . ALA A 1 11 ? -0.572 5.882 -3.762 1.00 97.24 11 A 1 ATOM 80 O O . ALA A 1 11 ? -0.696 7.049 -4.133 1.00 96.19 11 A 1 ATOM 81 C CB . ALA A 1 11 ? 1.546 5.031 -2.741 1.00 95.53 11 A 1 ATOM 82 N N . THR A 1 12 ? -1.050 4.858 -4.449 1.00 96.16 12 A 1 ATOM 83 C CA . THR A 1 12 ? -1.754 5.044 -5.716 1.00 96.16 12 A 1 ATOM 84 C C . THR A 1 12 ? -3.136 5.647 -5.496 1.00 96.81 12 A 1 ATOM 85 O O . THR A 1 12 ? -3.546 6.558 -6.218 1.00 95.55 12 A 1 ATOM 86 C CB . THR A 1 12 ? -1.896 3.708 -6.453 1.00 94.68 12 A 1 ATOM 87 O OG1 . THR A 1 12 ? -0.605 3.134 -6.655 1.00 90.46 12 A 1 ATOM 88 C CG2 . THR A 1 12 ? -2.567 3.905 -7.800 1.00 90.40 12 A 1 ATOM 89 N N . GLY A 1 13 ? -3.848 5.141 -4.500 1.00 94.85 13 A 1 ATOM 90 C CA . GLY A 1 13 ? -5.187 5.620 -4.199 1.00 94.88 13 A 1 ATOM 91 C C . GLY A 1 13 ? -5.201 7.056 -3.724 1.00 96.15 13 A 1 ATOM 92 O O . GLY A 1 13 ? -6.034 7.855 -4.153 1.00 95.65 13 A 1 ATOM 93 N N . ALA A 1 14 ? -4.274 7.397 -2.838 1.00 94.70 14 A 1 ATOM 94 C CA . ALA A 1 14 ? -4.177 8.751 -2.303 1.00 94.88 14 A 1 ATOM 95 C C . ALA A 1 14 ? -3.744 9.742 -3.374 1.00 95.88 14 A 1 ATOM 96 O O . ALA A 1 14 ? -4.201 10.884 -3.395 1.00 94.11 14 A 1 ATOM 97 C CB . ALA A 1 14 ? -3.196 8.786 -1.135 1.00 93.26 14 A 1 ATOM 98 N N . LEU A 1 15 ? -2.862 9.300 -4.258 1.00 93.54 15 A 1 ATOM 99 C CA . LEU A 1 15 ? -2.359 10.150 -5.334 1.00 93.67 15 A 1 ATOM 100 C C . LEU A 1 15 ? -3.426 10.402 -6.388 1.00 94.66 15 A 1 ATOM 101 O O . LEU A 1 15 ? -3.668 11.544 -6.792 1.00 93.12 15 A 1 ATOM 102 C CB . LEU A 1 15 ? -1.130 9.504 -5.977 1.00 91.64 15 A 1 ATOM 103 C CG . LEU A 1 15 ? -0.475 10.353 -7.067 1.00 87.26 15 A 1 ATOM 104 C CD1 . LEU A 1 15 ? 0.105 11.624 -6.483 1.00 84.57 15 A 1 ATOM 105 C CD2 . LEU A 1 15 ? 0.604 9.550 -7.781 1.00 82.85 15 A 1 ATOM 106 N N . ALA A 1 16 ? -4.054 9.313 -6.840 1.00 90.59 16 A 1 ATOM 107 C CA . ALA A 1 16 ? -5.066 9.415 -7.884 1.00 88.69 16 A 1 ATOM 108 C C . ALA A 1 16 ? -5.979 8.205 -7.836 1.00 87.58 16 A 1 ATOM 109 O O . ALA A 1 16 ? -7.172 8.374 -7.513 1.00 82.78 16 A 1 ATOM 110 C CB . ALA A 1 16 ? -4.408 9.544 -9.256 1.00 82.79 16 A 1 ATOM 111 O OXT . ALA A 1 16 ? -5.499 7.106 -8.116 1.00 75.56 16 A 1 #