# 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_spkb28482 # _entry.id spkb28482 # 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 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" "C5 H9 N O2" 115.130 PRO y PROLINE C1C[C@H](NC1)C(=O)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 ALA 3 1 n PHE 4 1 n ILE 5 1 n VAL 6 1 n LEU 7 1 n VAL 8 1 n ALA 9 1 n LEU 10 1 n ALA 11 1 n LEU 12 1 n ALA 13 1 n ALA 14 1 n PRO 15 1 n ALA 16 1 n LEU 17 1 n GLY 18 # _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 05:54:59)" _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 96.89 _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 93.34 1 1 A LYS 2 2 95.66 1 2 A ALA 3 2 98.79 1 3 A PHE 4 2 97.39 1 4 A ILE 5 2 98.00 1 5 A VAL 6 2 98.50 1 6 A LEU 7 2 97.19 1 7 A VAL 8 2 98.24 1 8 A ALA 9 2 98.40 1 9 A LEU 10 2 97.14 1 10 A ALA 11 2 98.14 1 11 A LEU 12 2 96.73 1 12 A ALA 13 2 98.29 1 13 A ALA 14 2 97.88 1 14 A PRO 15 2 97.59 1 15 A ALA 16 2 97.22 1 16 A LEU 17 2 94.86 1 17 A GLY 18 2 92.10 1 18 # _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 ALA . 3 A 3 A 4 1 n PHE . 4 A 4 A 5 1 n ILE . 5 A 5 A 6 1 n VAL . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n VAL . 8 A 8 A 9 1 n ALA . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n PRO . 15 A 15 A 16 1 n ALA . 16 A 16 A 17 1 n LEU . 17 A 17 A 18 1 n GLY . 18 A 18 # _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 ? -11.464 -0.593 7.286 1.00 97.14 1 A 1 ATOM 2 C CA . MET A 1 1 ? -11.104 0.727 6.741 1.00 97.61 1 A 1 ATOM 3 C C . MET A 1 1 ? -10.665 0.608 5.289 1.00 97.98 1 A 1 ATOM 4 O O . MET A 1 1 ? -10.021 -0.363 4.908 1.00 96.96 1 A 1 ATOM 5 C CB . MET A 1 1 ? -9.962 1.348 7.546 1.00 95.79 1 A 1 ATOM 6 C CG . MET A 1 1 ? -10.327 1.592 8.994 1.00 91.74 1 A 1 ATOM 7 S SD . MET A 1 1 ? -8.969 2.332 9.918 1.00 89.13 1 A 1 ATOM 8 C CE . MET A 1 1 ? -9.725 2.485 11.521 1.00 80.38 1 A 1 ATOM 9 N N . LYS A 1 2 ? -11.024 1.595 4.494 1.00 98.32 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -10.639 1.615 3.082 1.00 98.55 2 A 1 ATOM 11 C C . LYS A 1 2 ? -9.382 2.455 2.892 1.00 98.66 2 A 1 ATOM 12 O O . LYS A 1 2 ? -8.460 2.063 2.181 1.00 98.45 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -11.786 2.186 2.252 1.00 98.31 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -11.466 2.267 0.767 1.00 96.49 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -11.298 0.892 0.159 1.00 94.11 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -11.076 0.980 -1.338 1.00 91.38 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -10.978 -0.374 -1.954 1.00 86.67 2 A 1 ATOM 18 N N . ALA A 1 3 ? -9.351 3.624 3.525 1.00 98.78 3 A 1 ATOM 19 C CA . ALA A 1 3 ? -8.203 4.524 3.417 1.00 98.83 3 A 1 ATOM 20 C C . ALA A 1 3 ? -6.932 3.869 3.948 1.00 98.87 3 A 1 ATOM 21 O O . ALA A 1 3 ? -5.842 4.088 3.422 1.00 98.74 3 A 1 ATOM 22 C CB . ALA A 1 3 ? -8.478 5.814 4.173 1.00 98.71 3 A 1 ATOM 23 N N . PHE A 1 4 ? -7.079 3.049 4.986 1.00 98.78 4 A 1 ATOM 24 C CA . PHE A 1 4 ? -5.929 2.367 5.578 1.00 98.81 4 A 1 ATOM 25 C C . PHE A 1 4 ? -5.230 1.492 4.545 1.00 98.85 4 A 1 ATOM 26 O O . PHE A 1 4 ? -4.001 1.465 4.462 1.00 98.67 4 A 1 ATOM 27 C CB . PHE A 1 4 ? -6.377 1.512 6.760 1.00 98.67 4 A 1 ATOM 28 C CG . PHE A 1 4 ? -5.230 0.782 7.404 1.00 97.95 4 A 1 ATOM 29 C CD1 . PHE A 1 4 ? -4.294 1.468 8.161 1.00 96.68 4 A 1 ATOM 30 C CD2 . PHE A 1 4 ? -5.087 -0.585 7.240 1.00 96.52 4 A 1 ATOM 31 C CE1 . PHE A 1 4 ? -3.229 0.803 8.751 1.00 95.33 4 A 1 ATOM 32 C CE2 . PHE A 1 4 ? -4.020 -1.262 7.827 1.00 95.51 4 A 1 ATOM 33 C CZ . PHE A 1 4 ? -3.093 -0.565 8.584 1.00 95.51 4 A 1 ATOM 34 N N . ILE A 1 5 ? -6.018 0.776 3.754 1.00 98.82 5 A 1 ATOM 35 C CA . ILE A 1 5 ? -5.465 -0.097 2.724 1.00 98.78 5 A 1 ATOM 36 C C . ILE A 1 5 ? -4.676 0.718 1.710 1.00 98.77 5 A 1 ATOM 37 O O . ILE A 1 5 ? -3.610 0.309 1.245 1.00 98.61 5 A 1 ATOM 38 C CB . ILE A 1 5 ? -6.579 -0.879 2.017 1.00 98.68 5 A 1 ATOM 39 C CG1 . ILE A 1 5 ? -7.369 -1.711 3.028 1.00 97.85 5 A 1 ATOM 40 C CG2 . ILE A 1 5 ? -5.982 -1.777 0.935 1.00 97.59 5 A 1 ATOM 41 C CD1 . ILE A 1 5 ? -6.495 -2.710 3.778 1.00 94.88 5 A 1 ATOM 42 N N . VAL A 1 6 ? -5.209 1.860 1.361 1.00 98.82 6 A 1 ATOM 43 C CA . VAL A 1 6 ? -4.550 2.740 0.398 1.00 98.78 6 A 1 ATOM 44 C C . VAL A 1 6 ? -3.215 3.238 0.945 1.00 98.77 6 A 1 ATOM 45 O O . VAL A 1 6 ? -2.209 3.271 0.234 1.00 98.63 6 A 1 ATOM 46 C CB . VAL A 1 6 ? -5.442 3.941 0.054 1.00 98.64 6 A 1 ATOM 47 C CG1 . VAL A 1 6 ? -4.724 4.879 -0.913 1.00 98.03 6 A 1 ATOM 48 C CG2 . VAL A 1 6 ? -6.751 3.458 -0.550 1.00 97.86 6 A 1 ATOM 49 N N . LEU A 1 7 ? -3.207 3.614 2.210 1.00 98.73 7 A 1 ATOM 50 C CA . LEU A 1 7 ? -1.993 4.121 2.845 1.00 98.68 7 A 1 ATOM 51 C C . LEU A 1 7 ? -0.903 3.054 2.867 1.00 98.73 7 A 1 ATOM 52 O O . LEU A 1 7 ? 0.254 3.330 2.543 1.00 98.62 7 A 1 ATOM 53 C CB . LEU A 1 7 ? -2.306 4.567 4.276 1.00 98.48 7 A 1 ATOM 54 C CG . LEU A 1 7 ? -3.234 5.773 4.363 1.00 95.47 7 A 1 ATOM 55 C CD1 . LEU A 1 7 ? -3.591 6.054 5.818 1.00 94.25 7 A 1 ATOM 56 C CD2 . LEU A 1 7 ? -2.586 6.997 3.736 1.00 94.60 7 A 1 ATOM 57 N N . VAL A 1 8 ? -1.285 1.841 3.241 1.00 98.63 8 A 1 ATOM 58 C CA . VAL A 1 8 ? -0.331 0.737 3.303 1.00 98.58 8 A 1 ATOM 59 C C . VAL A 1 8 ? 0.189 0.395 1.913 1.00 98.58 8 A 1 ATOM 60 O O . VAL A 1 8 ? 1.392 0.202 1.716 1.00 98.42 8 A 1 ATOM 61 C CB . VAL A 1 8 ? -0.975 -0.504 3.933 1.00 98.39 8 A 1 ATOM 62 C CG1 . VAL A 1 8 ? -0.011 -1.680 3.901 1.00 97.61 8 A 1 ATOM 63 C CG2 . VAL A 1 8 ? -1.390 -0.206 5.363 1.00 97.49 8 A 1 ATOM 64 N N . ALA A 1 9 ? -0.722 0.305 0.961 1.00 98.54 9 A 1 ATOM 65 C CA . ALA A 1 9 ? -0.347 -0.024 -0.409 1.00 98.46 9 A 1 ATOM 66 C C . ALA A 1 9 ? 0.593 1.029 -0.984 1.00 98.46 9 A 1 ATOM 67 O O . ALA A 1 9 ? 1.555 0.700 -1.682 1.00 98.16 9 A 1 ATOM 68 C CB . ALA A 1 9 ? -1.596 -0.135 -1.273 1.00 98.36 9 A 1 ATOM 69 N N . LEU A 1 10 ? 0.315 2.272 -0.698 1.00 98.55 10 A 1 ATOM 70 C CA . LEU A 1 10 ? 1.137 3.375 -1.191 1.00 98.35 10 A 1 ATOM 71 C C . LEU A 1 10 ? 2.545 3.302 -0.614 1.00 98.42 10 A 1 ATOM 72 O O . LEU A 1 10 ? 3.534 3.433 -1.337 1.00 98.15 10 A 1 ATOM 73 C CB . LEU A 1 10 ? 0.505 4.712 -0.809 1.00 98.01 10 A 1 ATOM 74 C CG . LEU A 1 10 ? 1.266 5.924 -1.345 1.00 96.03 10 A 1 ATOM 75 C CD1 . LEU A 1 10 ? 1.192 5.979 -2.857 1.00 94.59 10 A 1 ATOM 76 C CD2 . LEU A 1 10 ? 0.720 7.205 -0.738 1.00 95.00 10 A 1 ATOM 77 N N . ALA A 1 11 ? 2.631 3.097 0.688 1.00 98.21 11 A 1 ATOM 78 C CA . ALA A 1 11 ? 3.923 3.021 1.359 1.00 98.18 11 A 1 ATOM 79 C C . ALA A 1 11 ? 4.717 1.814 0.888 1.00 98.32 11 A 1 ATOM 80 O O . ALA A 1 11 ? 5.933 1.896 0.702 1.00 97.99 11 A 1 ATOM 81 C CB . ALA A 1 11 ? 3.718 2.955 2.868 1.00 98.02 11 A 1 ATOM 82 N N . LEU A 1 12 ? 4.034 0.695 0.693 1.00 98.34 12 A 1 ATOM 83 C CA . LEU A 1 12 ? 4.688 -0.530 0.249 1.00 98.19 12 A 1 ATOM 84 C C . LEU A 1 12 ? 5.157 -0.404 -1.191 1.00 98.36 12 A 1 ATOM 85 O O . LEU A 1 12 ? 6.258 -0.836 -1.537 1.00 98.05 12 A 1 ATOM 86 C CB . LEU A 1 12 ? 3.727 -1.708 0.374 1.00 97.82 12 A 1 ATOM 87 C CG . LEU A 1 12 ? 4.363 -3.050 0.034 1.00 95.56 12 A 1 ATOM 88 C CD1 . LEU A 1 12 ? 5.472 -3.380 1.015 1.00 93.60 12 A 1 ATOM 89 C CD2 . LEU A 1 12 ? 3.317 -4.150 0.025 1.00 93.94 12 A 1 ATOM 90 N N . ALA A 1 13 ? 4.317 0.170 -2.026 1.00 98.32 13 A 1 ATOM 91 C CA . ALA A 1 13 ? 4.647 0.349 -3.434 1.00 98.34 13 A 1 ATOM 92 C C . ALA A 1 13 ? 5.854 1.260 -3.603 1.00 98.54 13 A 1 ATOM 93 O O . ALA A 1 13 ? 6.679 1.054 -4.495 1.00 98.21 13 A 1 ATOM 94 C CB . ALA A 1 13 ? 3.454 0.928 -4.184 1.00 98.05 13 A 1 ATOM 95 N N . ALA A 1 14 ? 5.956 2.259 -2.761 1.00 98.07 14 A 1 ATOM 96 C CA . ALA A 1 14 ? 7.074 3.198 -2.814 1.00 97.98 14 A 1 ATOM 97 C C . ALA A 1 14 ? 7.734 3.333 -1.451 1.00 98.27 14 A 1 ATOM 98 O O . ALA A 1 14 ? 7.508 4.313 -0.736 1.00 97.82 14 A 1 ATOM 99 C CB . ALA A 1 14 ? 6.582 4.557 -3.289 1.00 97.27 14 A 1 ATOM 100 N N . PRO A 1 15 ? 8.559 2.349 -1.076 1.00 98.23 15 A 1 ATOM 101 C CA . PRO A 1 15 ? 9.242 2.364 0.217 1.00 98.12 15 A 1 ATOM 102 C C . PRO A 1 15 ? 10.200 3.537 0.333 1.00 98.30 15 A 1 ATOM 103 O O . PRO A 1 15 ? 10.608 4.127 -0.669 1.00 97.51 15 A 1 ATOM 104 C CB . PRO A 1 15 ? 9.998 1.037 0.249 1.00 97.37 15 A 1 ATOM 105 C CG . PRO A 1 15 ? 10.187 0.683 -1.187 1.00 96.01 15 A 1 ATOM 106 C CD . PRO A 1 15 ? 8.953 1.200 -1.894 1.00 97.56 15 A 1 ATOM 107 N N . ALA A 1 16 ? 10.565 3.858 1.557 1.00 97.80 16 A 1 ATOM 108 C CA . ALA A 1 16 ? 11.468 4.976 1.799 1.00 97.50 16 A 1 ATOM 109 C C . ALA A 1 16 ? 12.875 4.620 1.342 1.00 97.59 16 A 1 ATOM 110 O O . ALA A 1 16 ? 13.742 4.293 2.151 1.00 96.44 16 A 1 ATOM 111 C CB . ALA A 1 16 ? 11.458 5.338 3.277 1.00 96.77 16 A 1 ATOM 112 N N . LEU A 1 17 ? 13.102 4.657 0.039 1.00 98.11 17 A 1 ATOM 113 C CA . LEU A 1 17 ? 14.399 4.348 -0.543 1.00 97.70 17 A 1 ATOM 114 C C . LEU A 1 17 ? 15.485 5.246 0.024 1.00 97.36 17 A 1 ATOM 115 O O . LEU A 1 17 ? 15.211 6.333 0.533 1.00 95.25 17 A 1 ATOM 116 C CB . LEU A 1 17 ? 14.365 4.512 -2.061 1.00 97.03 17 A 1 ATOM 117 C CG . LEU A 1 17 ? 14.117 5.944 -2.501 1.00 94.79 17 A 1 ATOM 118 C CD1 . LEU A 1 17 ? 14.735 6.173 -3.867 1.00 90.21 17 A 1 ATOM 119 C CD2 . LEU A 1 17 ? 12.641 6.258 -2.534 1.00 88.45 17 A 1 ATOM 120 N N . GLY A 1 18 ? 16.717 4.776 -0.091 1.00 96.15 18 A 1 ATOM 121 C CA . GLY A 1 18 ? 17.825 5.572 0.398 1.00 94.09 18 A 1 ATOM 122 C C . GLY A 1 18 ? 18.889 4.696 1.031 1.00 92.16 18 A 1 ATOM 123 O O . GLY A 1 18 ? 18.622 4.111 2.081 1.00 86.77 18 A 1 ATOM 124 O OXT . GLY A 1 18 ? 19.990 4.587 0.474 1.00 91.31 18 A 1 #