# 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_spkb36320 # _entry.id spkb36320 # 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" "C3 H7 N O2 S" 121.158 CYS y CYSTEINE C([C@@H](C(=O)O)N)S ? "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" "C11 H12 N2 O2" 204.225 TRP y TRYPTOPHAN c1ccc2c(c1)c(c[nH]2)C[C@@H](C(=O)O)N ? "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 TRP 4 1 n VAL 5 1 n ILE 6 1 n CYS 7 1 n LEU 8 1 n LEU 9 1 n VAL 10 1 n ILE 11 1 n CYS 12 1 n ALA 13 1 n ALA 14 1 n VAL 15 1 n ILE 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 @ 2025-07-03 05:13:28)" _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 95.50 _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 86.81 1 1 A LYS 2 2 89.85 1 2 A ALA 3 2 97.60 1 3 A TRP 4 2 95.15 1 4 A VAL 5 2 97.63 1 5 A ILE 6 2 96.98 1 6 A CYS 7 2 97.39 1 7 A LEU 8 2 96.33 1 8 A LEU 9 2 96.54 1 9 A VAL 10 2 97.99 1 10 A ILE 11 2 96.76 1 11 A CYS 12 2 97.34 1 12 A ALA 13 2 98.07 1 13 A ALA 14 2 98.40 1 14 A VAL 15 2 96.87 1 15 A ILE 16 2 95.20 1 16 A ALA 17 2 93.61 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 ALA . 3 A 3 A 4 1 n TRP . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n ILE . 6 A 6 A 7 1 n CYS . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n VAL . 10 A 10 A 11 1 n ILE . 11 A 11 A 12 1 n CYS . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n VAL . 15 A 15 A 16 1 n ILE . 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 ? -13.058 -3.656 6.634 1.00 92.64 1 A 1 ATOM 2 C CA . MET A 1 1 ? -11.697 -3.088 6.656 1.00 92.62 1 A 1 ATOM 3 C C . MET A 1 1 ? -11.035 -3.285 5.299 1.00 93.83 1 A 1 ATOM 4 O O . MET A 1 1 ? -11.070 -4.385 4.760 1.00 90.42 1 A 1 ATOM 5 C CB . MET A 1 1 ? -10.854 -3.778 7.726 1.00 89.23 1 A 1 ATOM 6 C CG . MET A 1 1 ? -11.437 -3.604 9.121 1.00 85.56 1 A 1 ATOM 7 S SD . MET A 1 1 ? -10.491 -4.497 10.354 1.00 79.75 1 A 1 ATOM 8 C CE . MET A 1 1 ? -11.563 -4.328 11.761 1.00 70.44 1 A 1 ATOM 9 N N . LYS A 1 2 ? -10.457 -2.248 4.741 1.00 95.35 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -9.792 -2.335 3.440 1.00 96.43 2 A 1 ATOM 11 C C . LYS A 1 2 ? -8.278 -2.250 3.621 1.00 97.19 2 A 1 ATOM 12 O O . LYS A 1 2 ? -7.695 -1.170 3.554 1.00 96.63 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -10.293 -1.237 2.515 1.00 94.90 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -11.682 -1.525 1.978 1.00 89.24 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -11.800 -1.102 0.537 1.00 85.27 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -13.166 -1.426 -0.020 1.00 80.06 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -13.198 -1.208 -1.486 1.00 73.54 2 A 1 ATOM 18 N N . ALA A 1 3 ? -7.658 -3.387 3.846 1.00 97.23 3 A 1 ATOM 19 C CA . ALA A 1 3 ? -6.204 -3.454 3.993 1.00 97.80 3 A 1 ATOM 20 C C . ALA A 1 3 ? -5.497 -3.254 2.652 1.00 98.15 3 A 1 ATOM 21 O O . ALA A 1 3 ? -4.347 -2.820 2.608 1.00 97.64 3 A 1 ATOM 22 C CB . ALA A 1 3 ? -5.822 -4.793 4.606 1.00 97.16 3 A 1 ATOM 23 N N . TRP A 1 4 ? -6.206 -3.562 1.554 1.00 97.27 4 A 1 ATOM 24 C CA . TRP A 1 4 ? -5.643 -3.432 0.211 1.00 97.40 4 A 1 ATOM 25 C C . TRP A 1 4 ? -5.313 -1.988 -0.132 1.00 97.72 4 A 1 ATOM 26 O O . TRP A 1 4 ? -4.303 -1.711 -0.774 1.00 97.29 4 A 1 ATOM 27 C CB . TRP A 1 4 ? -6.615 -4.019 -0.811 1.00 97.08 4 A 1 ATOM 28 C CG . TRP A 1 4 ? -6.445 -5.491 -0.966 1.00 96.17 4 A 1 ATOM 29 C CD1 . TRP A 1 4 ? -7.110 -6.459 -0.294 1.00 93.76 4 A 1 ATOM 30 C CD2 . TRP A 1 4 ? -5.525 -6.175 -1.851 1.00 95.21 4 A 1 ATOM 31 N NE1 . TRP A 1 4 ? -6.663 -7.698 -0.705 1.00 93.82 4 A 1 ATOM 32 C CE2 . TRP A 1 4 ? -5.690 -7.553 -1.661 1.00 95.50 4 A 1 ATOM 33 C CE3 . TRP A 1 4 ? -4.585 -5.728 -2.788 1.00 94.46 4 A 1 ATOM 34 C CZ2 . TRP A 1 4 ? -4.942 -8.488 -2.382 1.00 93.70 4 A 1 ATOM 35 C CZ3 . TRP A 1 4 ? -3.844 -6.664 -3.502 1.00 91.36 4 A 1 ATOM 36 C CH2 . TRP A 1 4 ? -4.026 -8.029 -3.294 1.00 91.30 4 A 1 ATOM 37 N N . VAL A 1 5 ? -6.151 -1.065 0.295 1.00 98.04 5 A 1 ATOM 38 C CA . VAL A 1 5 ? -5.923 0.358 0.042 1.00 98.20 5 A 1 ATOM 39 C C . VAL A 1 5 ? -4.648 0.819 0.743 1.00 98.31 5 A 1 ATOM 40 O O . VAL A 1 5 ? -3.870 1.599 0.197 1.00 98.17 5 A 1 ATOM 41 C CB . VAL A 1 5 ? -7.120 1.194 0.508 1.00 97.98 5 A 1 ATOM 42 C CG1 . VAL A 1 5 ? -6.878 2.674 0.257 1.00 96.51 5 A 1 ATOM 43 C CG2 . VAL A 1 5 ? -8.380 0.750 -0.219 1.00 96.22 5 A 1 ATOM 44 N N . ILE A 1 6 ? -4.439 0.328 1.947 1.00 98.04 6 A 1 ATOM 45 C CA . ILE A 1 6 ? -3.241 0.661 2.711 1.00 98.01 6 A 1 ATOM 46 C C . ILE A 1 6 ? -2.004 0.124 1.999 1.00 98.11 6 A 1 ATOM 47 O O . ILE A 1 6 ? -0.994 0.821 1.871 1.00 98.00 6 A 1 ATOM 48 C CB . ILE A 1 6 ? -3.333 0.088 4.136 1.00 97.92 6 A 1 ATOM 49 C CG1 . ILE A 1 6 ? -4.633 0.537 4.831 1.00 96.64 6 A 1 ATOM 50 C CG2 . ILE A 1 6 ? -2.112 0.516 4.956 1.00 96.41 6 A 1 ATOM 51 C CD1 . ILE A 1 6 ? -4.774 2.050 4.925 1.00 92.72 6 A 1 ATOM 52 N N . CYS A 1 7 ? -2.086 -1.108 1.521 1.00 97.98 7 A 1 ATOM 53 C CA . CYS A 1 7 ? -0.979 -1.718 0.791 1.00 98.00 7 A 1 ATOM 54 C C . CYS A 1 7 ? -0.644 -0.914 -0.463 1.00 98.13 7 A 1 ATOM 55 O O . CYS A 1 7 ? 0.523 -0.693 -0.767 1.00 97.74 7 A 1 ATOM 56 C CB . CYS A 1 7 ? -1.333 -3.155 0.415 1.00 97.69 7 A 1 ATOM 57 S SG . CYS A 1 7 ? -1.402 -4.239 1.858 1.00 94.82 7 A 1 ATOM 58 N N . LEU A 1 8 ? -1.676 -0.457 -1.164 1.00 97.94 8 A 1 ATOM 59 C CA . LEU A 1 8 ? -1.481 0.346 -2.370 1.00 98.05 8 A 1 ATOM 60 C C . LEU A 1 8 ? -0.712 1.626 -2.063 1.00 98.28 8 A 1 ATOM 61 O O . LEU A 1 8 ? 0.211 1.992 -2.793 1.00 98.18 8 A 1 ATOM 62 C CB . LEU A 1 8 ? -2.845 0.680 -2.983 1.00 97.96 8 A 1 ATOM 63 C CG . LEU A 1 8 ? -3.250 -0.293 -4.086 1.00 94.94 8 A 1 ATOM 64 C CD1 . LEU A 1 8 ? -4.756 -0.237 -4.321 1.00 92.10 8 A 1 ATOM 65 C CD2 . LEU A 1 8 ? -2.519 0.031 -5.375 1.00 93.18 8 A 1 ATOM 66 N N . LEU A 1 9 ? -1.081 2.293 -0.990 1.00 98.01 9 A 1 ATOM 67 C CA . LEU A 1 9 ? -0.406 3.524 -0.589 1.00 98.06 9 A 1 ATOM 68 C C . LEU A 1 9 ? 1.054 3.257 -0.234 1.00 98.29 9 A 1 ATOM 69 O O . LEU A 1 9 ? 1.941 4.021 -0.617 1.00 98.20 9 A 1 ATOM 70 C CB . LEU A 1 9 ? -1.136 4.144 0.604 1.00 97.93 9 A 1 ATOM 71 C CG . LEU A 1 9 ? -2.477 4.783 0.241 1.00 95.23 9 A 1 ATOM 72 C CD1 . LEU A 1 9 ? -3.263 5.112 1.498 1.00 92.93 9 A 1 ATOM 73 C CD2 . LEU A 1 9 ? -2.261 6.051 -0.580 1.00 93.65 9 A 1 ATOM 74 N N . VAL A 1 10 ? 1.297 2.179 0.485 1.00 98.40 10 A 1 ATOM 75 C CA . VAL A 1 10 ? 2.654 1.812 0.884 1.00 98.39 10 A 1 ATOM 76 C C . VAL A 1 10 ? 3.498 1.467 -0.340 1.00 98.54 10 A 1 ATOM 77 O O . VAL A 1 10 ? 4.650 1.898 -0.449 1.00 98.35 10 A 1 ATOM 78 C CB . VAL A 1 10 ? 2.628 0.639 1.874 1.00 98.06 10 A 1 ATOM 79 C CG1 . VAL A 1 10 ? 4.038 0.163 2.199 1.00 97.19 10 A 1 ATOM 80 C CG2 . VAL A 1 10 ? 1.926 1.054 3.160 1.00 97.02 10 A 1 ATOM 81 N N . ILE A 1 11 ? 2.929 0.711 -1.264 1.00 98.07 11 A 1 ATOM 82 C CA . ILE A 1 11 ? 3.635 0.324 -2.482 1.00 98.04 11 A 1 ATOM 83 C C . ILE A 1 11 ? 3.947 1.556 -3.324 1.00 98.28 11 A 1 ATOM 84 O O . ILE A 1 11 ? 5.062 1.712 -3.823 1.00 98.04 11 A 1 ATOM 85 C CB . ILE A 1 11 ? 2.807 -0.695 -3.284 1.00 97.67 11 A 1 ATOM 86 C CG1 . ILE A 1 11 ? 2.661 -2.021 -2.509 1.00 96.13 11 A 1 ATOM 87 C CG2 . ILE A 1 11 ? 3.447 -0.961 -4.647 1.00 95.87 11 A 1 ATOM 88 C CD1 . ILE A 1 11 ? 3.973 -2.755 -2.294 1.00 91.99 11 A 1 ATOM 89 N N . CYS A 1 12 ? 2.979 2.441 -3.482 1.00 98.14 12 A 1 ATOM 90 C CA . CYS A 1 12 ? 3.182 3.669 -4.243 1.00 98.13 12 A 1 ATOM 91 C C . CYS A 1 12 ? 4.302 4.506 -3.637 1.00 98.37 12 A 1 ATOM 92 O O . CYS A 1 12 ? 5.152 5.024 -4.353 1.00 97.90 12 A 1 ATOM 93 C CB . CYS A 1 12 ? 1.885 4.471 -4.285 1.00 97.60 12 A 1 ATOM 94 S SG . CYS A 1 12 ? 0.693 3.747 -5.422 1.00 93.91 12 A 1 ATOM 95 N N . ALA A 1 13 ? 4.293 4.629 -2.326 1.00 98.01 13 A 1 ATOM 96 C CA . ALA A 1 13 ? 5.331 5.383 -1.633 1.00 98.15 13 A 1 ATOM 97 C C . ALA A 1 13 ? 6.702 4.741 -1.825 1.00 98.39 13 A 1 ATOM 98 O O . ALA A 1 13 ? 7.697 5.439 -2.015 1.00 98.02 13 A 1 ATOM 99 C CB . ALA A 1 13 ? 4.987 5.474 -0.154 1.00 97.80 13 A 1 ATOM 100 N N . ALA A 1 14 ? 6.751 3.423 -1.783 1.00 98.50 14 A 1 ATOM 101 C CA . ALA A 1 14 ? 8.003 2.692 -1.965 1.00 98.48 14 A 1 ATOM 102 C C . ALA A 1 14 ? 8.527 2.831 -3.392 1.00 98.59 14 A 1 ATOM 103 O O . ALA A 1 14 ? 9.737 2.923 -3.603 1.00 98.22 14 A 1 ATOM 104 C CB . ALA A 1 14 ? 7.796 1.227 -1.614 1.00 98.20 14 A 1 ATOM 105 N N . VAL A 1 15 ? 7.631 2.861 -4.372 1.00 98.14 15 A 1 ATOM 106 C CA . VAL A 1 15 ? 8.015 3.001 -5.777 1.00 97.99 15 A 1 ATOM 107 C C . VAL A 1 15 ? 8.515 4.413 -6.068 1.00 98.14 15 A 1 ATOM 108 O O . VAL A 1 15 ? 9.478 4.598 -6.817 1.00 97.53 15 A 1 ATOM 109 C CB . VAL A 1 15 ? 6.839 2.645 -6.698 1.00 97.30 15 A 1 ATOM 110 C CG1 . VAL A 1 15 ? 7.161 2.957 -8.155 1.00 94.45 15 A 1 ATOM 111 C CG2 . VAL A 1 15 ? 6.500 1.170 -6.569 1.00 94.51 15 A 1 ATOM 112 N N . ILE A 1 16 ? 7.854 5.400 -5.507 1.00 97.56 16 A 1 ATOM 113 C CA . ILE A 1 16 ? 8.236 6.793 -5.712 1.00 97.30 16 A 1 ATOM 114 C C . ILE A 1 16 ? 9.529 7.121 -4.969 1.00 97.47 16 A 1 ATOM 115 O O . ILE A 1 16 ? 10.378 7.849 -5.483 1.00 97.06 16 A 1 ATOM 116 C CB . ILE A 1 16 ? 7.099 7.729 -5.264 1.00 96.64 16 A 1 ATOM 117 C CG1 . ILE A 1 16 ? 5.864 7.530 -6.150 1.00 94.42 16 A 1 ATOM 118 C CG2 . ILE A 1 16 ? 7.554 9.187 -5.338 1.00 93.37 16 A 1 ATOM 119 C CD1 . ILE A 1 16 ? 4.594 8.106 -5.551 1.00 87.81 16 A 1 ATOM 120 N N . ALA A 1 17 ? 9.658 6.594 -3.778 1.00 96.78 17 A 1 ATOM 121 C CA . ALA A 1 17 ? 10.834 6.837 -2.949 1.00 96.33 17 A 1 ATOM 122 C C . ALA A 1 17 ? 12.037 6.058 -3.468 1.00 95.64 17 A 1 ATOM 123 O O . ALA A 1 17 ? 13.167 6.566 -3.357 1.00 92.11 17 A 1 ATOM 124 C CB . ALA A 1 17 ? 10.532 6.465 -1.501 1.00 94.64 17 A 1 ATOM 125 O OXT . ALA A 1 17 ? 11.868 4.942 -3.958 1.00 86.13 17 A 1 #