# 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_spkb34264 # _entry.id spkb34264 # 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 H15 N4 O2" 175.209 ARG y ARGININE C(C[C@@H](C(=O)O)N)CNC(=[NH2+])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" "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" "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 ILE 2 1 n ARG 3 1 n LYS 4 1 n THR 5 1 n LEU 6 1 n ALA 7 1 n ALA 8 1 n SER 9 1 n CYS 10 1 n ALA 11 1 n VAL 12 1 n LEU 13 1 n LEU 14 1 n MET 15 1 n ALA 16 1 n GLY 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 @ 2025-07-11 16:35:38)" _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 96.16 _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 93.13 1 1 A ILE 2 2 96.33 1 2 A ARG 3 2 90.89 1 3 A LYS 4 2 95.20 1 4 A THR 5 2 97.75 1 5 A LEU 6 2 96.59 1 6 A ALA 7 2 98.74 1 7 A ALA 8 2 98.77 1 8 A SER 9 2 97.39 1 9 A CYS 10 2 97.94 1 10 A ALA 11 2 98.81 1 11 A VAL 12 2 98.53 1 12 A LEU 13 2 97.53 1 13 A LEU 14 2 97.19 1 14 A MET 15 2 94.52 1 15 A ALA 16 2 98.27 1 16 A GLY 17 2 93.01 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 ILE . 2 A 2 A 3 1 n ARG . 3 A 3 A 4 1 n LYS . 4 A 4 A 5 1 n THR . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n SER . 9 A 9 A 10 1 n CYS . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n VAL . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n MET . 15 A 15 A 16 1 n ALA . 16 A 16 A 17 1 n GLY . 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 ? -3.761 -7.121 11.818 1.00 97.48 1 A 1 ATOM 2 C CA . MET A 1 1 ? -2.525 -6.551 11.259 1.00 97.65 1 A 1 ATOM 3 C C . MET A 1 1 ? -2.826 -5.796 9.970 1.00 97.98 1 A 1 ATOM 4 O O . MET A 1 1 ? -3.111 -6.409 8.944 1.00 96.77 1 A 1 ATOM 5 C CB . MET A 1 1 ? -1.505 -7.661 10.974 1.00 95.99 1 A 1 ATOM 6 C CG . MET A 1 1 ? -0.832 -8.178 12.233 1.00 90.86 1 A 1 ATOM 7 S SD . MET A 1 1 ? 0.312 -9.513 11.884 1.00 88.61 1 A 1 ATOM 8 C CE . MET A 1 1 ? 1.082 -9.716 13.472 1.00 79.69 1 A 1 ATOM 9 N N . ILE A 1 2 ? -2.768 -4.479 10.028 1.00 97.80 2 A 1 ATOM 10 C CA . ILE A 1 2 ? -3.054 -3.646 8.863 1.00 98.14 2 A 1 ATOM 11 C C . ILE A 1 2 ? -1.887 -2.690 8.614 1.00 98.43 2 A 1 ATOM 12 O O . ILE A 1 2 ? -1.966 -1.492 8.899 1.00 98.20 2 A 1 ATOM 13 C CB . ILE A 1 2 ? -4.342 -2.856 9.068 1.00 97.85 2 A 1 ATOM 14 C CG1 . ILE A 1 2 ? -5.492 -3.761 9.515 1.00 94.88 2 A 1 ATOM 15 C CG2 . ILE A 1 2 ? -4.723 -2.144 7.761 1.00 94.66 2 A 1 ATOM 16 C CD1 . ILE A 1 2 ? -6.685 -2.977 10.025 1.00 90.65 2 A 1 ATOM 17 N N . ARG A 1 3 ? -0.813 -3.233 8.103 1.00 98.54 3 A 1 ATOM 18 C CA . ARG A 1 3 ? 0.379 -2.434 7.813 1.00 98.64 3 A 1 ATOM 19 C C . ARG A 1 3 ? 0.728 -2.473 6.331 1.00 98.71 3 A 1 ATOM 20 O O . ARG A 1 3 ? 1.258 -1.503 5.787 1.00 98.39 3 A 1 ATOM 21 C CB . ARG A 1 3 ? 1.563 -2.920 8.660 1.00 98.35 3 A 1 ATOM 22 C CG . ARG A 1 3 ? 1.930 -4.379 8.415 1.00 95.09 3 A 1 ATOM 23 C CD . ARG A 1 3 ? 2.997 -4.828 9.391 1.00 91.93 3 A 1 ATOM 24 N NE . ARG A 1 3 ? 3.345 -6.238 9.213 1.00 85.20 3 A 1 ATOM 25 C CZ . ARG A 1 3 ? 4.156 -6.908 10.026 1.00 82.86 3 A 1 ATOM 26 N NH1 . ARG A 1 3 ? 4.705 -6.319 11.071 1.00 76.55 3 A 1 ATOM 27 N NH2 . ARG A 1 3 ? 4.418 -8.181 9.789 1.00 75.58 3 A 1 ATOM 28 N N . LYS A 1 4 ? 0.416 -3.590 5.695 1.00 98.56 4 A 1 ATOM 29 C CA . LYS A 1 4 ? 0.691 -3.757 4.273 1.00 98.59 4 A 1 ATOM 30 C C . LYS A 1 4 ? -0.205 -2.835 3.454 1.00 98.68 4 A 1 ATOM 31 O O . LYS A 1 4 ? 0.249 -2.189 2.509 1.00 98.47 4 A 1 ATOM 32 C CB . LYS A 1 4 ? 0.482 -5.221 3.869 1.00 98.40 4 A 1 ATOM 33 C CG . LYS A 1 4 ? 1.416 -5.663 2.750 1.00 96.05 4 A 1 ATOM 34 C CD . LYS A 1 4 ? 2.798 -6.029 3.289 1.00 94.01 4 A 1 ATOM 35 C CE . LYS A 1 4 ? 3.749 -6.419 2.172 1.00 89.83 4 A 1 ATOM 36 N NZ . LYS A 1 4 ? 5.075 -6.866 2.695 1.00 84.17 4 A 1 ATOM 37 N N . THR A 1 5 ? -1.464 -2.775 3.835 1.00 98.79 5 A 1 ATOM 38 C CA . THR A 1 5 ? -2.435 -1.935 3.147 1.00 98.79 5 A 1 ATOM 39 C C . THR A 1 5 ? -2.106 -0.457 3.338 1.00 98.80 5 A 1 ATOM 40 O O . THR A 1 5 ? -2.145 0.328 2.389 1.00 98.62 5 A 1 ATOM 41 C CB . THR A 1 5 ? -3.849 -2.221 3.663 1.00 98.71 5 A 1 ATOM 42 O OG1 . THR A 1 5 ? -4.068 -3.626 3.724 1.00 95.79 5 A 1 ATOM 43 C CG2 . THR A 1 5 ? -4.892 -1.598 2.749 1.00 94.74 5 A 1 ATOM 44 N N . LEU A 1 6 ? -1.769 -0.093 4.554 1.00 98.79 6 A 1 ATOM 45 C CA . LEU A 1 6 ? -1.423 1.290 4.865 1.00 98.75 6 A 1 ATOM 46 C C . LEU A 1 6 ? -0.141 1.705 4.155 1.00 98.81 6 A 1 ATOM 47 O O . LEU A 1 6 ? -0.061 2.799 3.593 1.00 98.69 6 A 1 ATOM 48 C CB . LEU A 1 6 ? -1.263 1.449 6.376 1.00 98.63 6 A 1 ATOM 49 C CG . LEU A 1 6 ? -2.573 1.367 7.155 1.00 95.36 6 A 1 ATOM 50 C CD1 . LEU A 1 6 ? -2.291 1.189 8.637 1.00 91.54 6 A 1 ATOM 51 C CD2 . LEU A 1 6 ? -3.403 2.623 6.930 1.00 92.17 6 A 1 ATOM 52 N N . ALA A 1 7 ? 0.839 0.826 4.181 1.00 98.78 7 A 1 ATOM 53 C CA . ALA A 1 7 ? 2.117 1.092 3.528 1.00 98.78 7 A 1 ATOM 54 C C . ALA A 1 7 ? 1.944 1.209 2.020 1.00 98.81 7 A 1 ATOM 55 O O . ALA A 1 7 ? 2.511 2.104 1.389 1.00 98.66 7 A 1 ATOM 56 C CB . ALA A 1 7 ? 3.103 -0.018 3.860 1.00 98.65 7 A 1 ATOM 57 N N . ALA A 1 8 ? 1.153 0.310 1.455 1.00 98.84 8 A 1 ATOM 58 C CA . ALA A 1 8 ? 0.897 0.315 0.021 1.00 98.81 8 A 1 ATOM 59 C C . ALA A 1 8 ? 0.150 1.578 -0.391 1.00 98.83 8 A 1 ATOM 60 O O . ALA A 1 8 ? 0.488 2.212 -1.389 1.00 98.67 8 A 1 ATOM 61 C CB . ALA A 1 8 ? 0.101 -0.925 -0.362 1.00 98.70 8 A 1 ATOM 62 N N . SER A 1 9 ? -0.855 1.936 0.387 1.00 98.84 9 A 1 ATOM 63 C CA . SER A 1 9 ? -1.653 3.125 0.113 1.00 98.79 9 A 1 ATOM 64 C C . SER A 1 9 ? -0.791 4.381 0.176 1.00 98.83 9 A 1 ATOM 65 O O . SER A 1 9 ? -0.888 5.260 -0.681 1.00 98.70 9 A 1 ATOM 66 C CB . SER A 1 9 ? -2.802 3.229 1.111 1.00 98.54 9 A 1 ATOM 67 O OG . SER A 1 9 ? -3.720 4.212 0.701 1.00 90.66 9 A 1 ATOM 68 N N . CYS A 1 10 ? 0.058 4.450 1.165 1.00 98.83 10 A 1 ATOM 69 C CA . CYS A 1 10 ? 0.944 5.592 1.337 1.00 98.81 10 A 1 ATOM 70 C C . CYS A 1 10 ? 1.981 5.651 0.218 1.00 98.85 10 A 1 ATOM 71 O O . CYS A 1 10 ? 2.320 6.727 -0.272 1.00 98.69 10 A 1 ATOM 72 C CB . CYS A 1 10 ? 1.635 5.507 2.696 1.00 98.60 10 A 1 ATOM 73 S SG . CYS A 1 10 ? 1.904 7.134 3.423 1.00 93.87 10 A 1 ATOM 74 N N . ALA A 1 11 ? 2.466 4.489 -0.179 1.00 98.85 11 A 1 ATOM 75 C CA . ALA A 1 11 ? 3.449 4.397 -1.257 1.00 98.84 11 A 1 ATOM 76 C C . ALA A 1 11 ? 2.872 4.923 -2.567 1.00 98.89 11 A 1 ATOM 77 O O . ALA A 1 11 ? 3.549 5.626 -3.319 1.00 98.76 11 A 1 ATOM 78 C CB . ALA A 1 11 ? 3.902 2.953 -1.422 1.00 98.70 11 A 1 ATOM 79 N N . VAL A 1 12 ? 1.619 4.578 -2.832 1.00 98.89 12 A 1 ATOM 80 C CA . VAL A 1 12 ? 0.936 5.032 -4.042 1.00 98.88 12 A 1 ATOM 81 C C . VAL A 1 12 ? 0.809 6.551 -4.032 1.00 98.91 12 A 1 ATOM 82 O O . VAL A 1 12 ? 1.009 7.216 -5.052 1.00 98.79 12 A 1 ATOM 83 C CB . VAL A 1 12 ? -0.456 4.384 -4.169 1.00 98.74 12 A 1 ATOM 84 C CG1 . VAL A 1 12 ? -1.218 4.941 -5.364 1.00 97.68 12 A 1 ATOM 85 C CG2 . VAL A 1 12 ? -0.321 2.875 -4.310 1.00 97.79 12 A 1 ATOM 86 N N . LEU A 1 13 ? 0.480 7.086 -2.880 1.00 98.82 13 A 1 ATOM 87 C CA . LEU A 1 13 ? 0.339 8.531 -2.729 1.00 98.78 13 A 1 ATOM 88 C C . LEU A 1 13 ? 1.679 9.230 -2.928 1.00 98.83 13 A 1 ATOM 89 O O . LEU A 1 13 ? 1.733 10.325 -3.493 1.00 98.60 13 A 1 ATOM 90 C CB . LEU A 1 13 ? -0.224 8.857 -1.344 1.00 98.61 13 A 1 ATOM 91 C CG . LEU A 1 13 ? -1.688 8.469 -1.153 1.00 97.28 13 A 1 ATOM 92 C CD1 . LEU A 1 13 ? -2.058 8.518 0.322 1.00 94.94 13 A 1 ATOM 93 C CD2 . LEU A 1 13 ? -2.595 9.399 -1.948 1.00 94.42 13 A 1 ATOM 94 N N . LEU A 1 14 ? 2.742 8.597 -2.481 1.00 98.71 14 A 1 ATOM 95 C CA . LEU A 1 14 ? 4.084 9.148 -2.633 1.00 98.65 14 A 1 ATOM 96 C C . LEU A 1 14 ? 4.495 9.178 -4.095 1.00 98.71 14 A 1 ATOM 97 O O . LEU A 1 14 ? 5.161 10.115 -4.544 1.00 98.31 14 A 1 ATOM 98 C CB . LEU A 1 14 ? 5.076 8.317 -1.822 1.00 98.39 14 A 1 ATOM 99 C CG . LEU A 1 14 ? 4.977 8.548 -0.315 1.00 96.70 14 A 1 ATOM 100 C CD1 . LEU A 1 14 ? 5.716 7.450 0.433 1.00 94.37 14 A 1 ATOM 101 C CD2 . LEU A 1 14 ? 5.558 9.906 0.047 1.00 93.71 14 A 1 ATOM 102 N N . MET A 1 15 ? 4.099 8.149 -4.832 1.00 98.58 15 A 1 ATOM 103 C CA . MET A 1 15 ? 4.411 8.070 -6.255 1.00 98.50 15 A 1 ATOM 104 C C . MET A 1 15 ? 3.593 9.081 -7.049 1.00 98.56 15 A 1 ATOM 105 O O . MET A 1 15 ? 4.074 9.654 -8.025 1.00 98.01 15 A 1 ATOM 106 C CB . MET A 1 15 ? 4.136 6.657 -6.776 1.00 98.05 15 A 1 ATOM 107 C CG . MET A 1 15 ? 5.206 5.664 -6.373 1.00 95.45 15 A 1 ATOM 108 S SD . MET A 1 15 ? 5.725 4.650 -7.750 1.00 89.12 15 A 1 ATOM 109 C CE . MET A 1 15 ? 7.151 3.846 -7.042 1.00 79.86 15 A 1 ATOM 110 N N . ALA A 1 16 ? 2.359 9.276 -6.638 1.00 98.58 16 A 1 ATOM 111 C CA . ALA A 1 16 ? 1.468 10.214 -7.310 1.00 98.49 16 A 1 ATOM 112 C C . ALA A 1 16 ? 1.746 11.648 -6.881 1.00 98.54 16 A 1 ATOM 113 O O . ALA A 1 16 ? 1.574 12.584 -7.667 1.00 97.74 16 A 1 ATOM 114 C CB . ALA A 1 16 ? 0.013 9.843 -7.026 1.00 98.01 16 A 1 ATOM 115 N N . GLY A 1 17 ? 2.143 11.815 -5.647 1.00 96.85 17 A 1 ATOM 116 C CA . GLY A 1 17 ? 2.440 13.138 -5.099 1.00 94.90 17 A 1 ATOM 117 C C . GLY A 1 17 ? 3.843 13.579 -5.392 1.00 92.98 17 A 1 ATOM 118 O O . GLY A 1 17 ? 4.025 14.443 -6.269 1.00 87.95 17 A 1 ATOM 119 O OXT . GLY A 1 17 ? 4.741 13.065 -4.731 1.00 92.39 17 A 1 #