# 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_spkb34262 # _entry.id spkb34262 # 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 "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" "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" "C9 H11 N O3" 181.189 TYR y TYROSINE c1cc(ccc1C[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 TYR 2 1 n LEU 3 1 n VAL 4 1 n PHE 5 1 n GLY 6 1 n ILE 7 1 n ILE 8 1 n PHE 9 1 n THR 10 1 n SER 11 1 n VAL 12 1 n ILE 13 1 n VAL 14 1 n THR 15 1 n SER 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 05:50:30)" _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 87.50 _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 81.53 1 1 A TYR 2 2 80.81 1 2 A LEU 3 2 85.49 1 3 A VAL 4 2 88.31 1 4 A PHE 5 2 83.37 1 5 A GLY 6 2 91.62 1 6 A ILE 7 2 91.84 1 7 A ILE 8 2 90.39 1 8 A PHE 9 2 86.43 1 9 A THR 10 2 89.00 1 10 A SER 11 2 90.05 1 11 A VAL 12 2 91.82 1 12 A ILE 13 2 92.53 1 13 A VAL 14 2 91.41 1 14 A THR 15 2 88.69 1 15 A SER 16 2 85.97 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 TYR . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n VAL . 4 A 4 A 5 1 n PHE . 5 A 5 A 6 1 n GLY . 6 A 6 A 7 1 n ILE . 7 A 7 A 8 1 n ILE . 8 A 8 A 9 1 n PHE . 9 A 9 A 10 1 n THR . 10 A 10 A 11 1 n SER . 11 A 11 A 12 1 n VAL . 12 A 12 A 13 1 n ILE . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n THR . 15 A 15 A 16 1 n SER . 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 ? 0.629 -8.008 7.058 1.00 86.05 1 A 1 ATOM 2 C CA . MET A 1 1 ? 1.737 -8.516 6.224 1.00 88.55 1 A 1 ATOM 3 C C . MET A 1 1 ? 1.988 -7.551 5.063 1.00 88.43 1 A 1 ATOM 4 O O . MET A 1 1 ? 1.516 -6.417 5.072 1.00 86.12 1 A 1 ATOM 5 C CB . MET A 1 1 ? 1.403 -9.908 5.696 1.00 83.02 1 A 1 ATOM 6 C CG . MET A 1 1 ? 1.143 -10.915 6.823 1.00 77.79 1 A 1 ATOM 7 S SD . MET A 1 1 ? -0.350 -10.519 7.752 1.00 74.73 1 A 1 ATOM 8 C CE . MET A 1 1 ? -0.342 -11.870 8.939 1.00 67.51 1 A 1 ATOM 9 N N . TYR A 1 2 ? 2.744 -8.020 4.068 1.00 81.70 2 A 1 ATOM 10 C CA . TYR A 1 2 ? 3.063 -7.186 2.904 1.00 85.46 2 A 1 ATOM 11 C C . TYR A 1 2 ? 1.817 -6.869 2.077 1.00 88.19 2 A 1 ATOM 12 O O . TYR A 1 2 ? 1.724 -5.804 1.470 1.00 86.94 2 A 1 ATOM 13 C CB . TYR A 1 2 ? 4.115 -7.873 2.032 1.00 82.83 2 A 1 ATOM 14 C CG . TYR A 1 2 ? 3.894 -9.370 1.895 1.00 79.28 2 A 1 ATOM 15 C CD1 . TYR A 1 2 ? 2.996 -9.870 0.965 1.00 79.86 2 A 1 ATOM 16 C CD2 . TYR A 1 2 ? 4.592 -10.258 2.703 1.00 77.91 2 A 1 ATOM 17 C CE1 . TYR A 1 2 ? 2.795 -11.234 0.845 1.00 76.87 2 A 1 ATOM 18 C CE2 . TYR A 1 2 ? 4.389 -11.627 2.582 1.00 76.97 2 A 1 ATOM 19 C CZ . TYR A 1 2 ? 3.493 -12.105 1.655 1.00 78.42 2 A 1 ATOM 20 O OH . TYR A 1 2 ? 3.292 -13.456 1.536 1.00 75.28 2 A 1 ATOM 21 N N . LEU A 1 3 ? 0.860 -7.774 2.063 1.00 86.44 3 A 1 ATOM 22 C CA . LEU A 1 3 ? -0.385 -7.575 1.321 1.00 89.75 3 A 1 ATOM 23 C C . LEU A 1 3 ? -1.192 -6.424 1.911 1.00 92.14 3 A 1 ATOM 24 O O . LEU A 1 3 ? -1.797 -5.635 1.187 1.00 90.92 3 A 1 ATOM 25 C CB . LEU A 1 3 ? -1.225 -8.856 1.329 1.00 87.83 3 A 1 ATOM 26 C CG . LEU A 1 3 ? -0.889 -9.841 0.212 1.00 81.67 3 A 1 ATOM 27 C CD1 . LEU A 1 3 ? 0.509 -10.418 0.407 1.00 78.85 3 A 1 ATOM 28 C CD2 . LEU A 1 3 ? -1.917 -10.952 0.152 1.00 76.34 3 A 1 ATOM 29 N N . VAL A 1 4 ? -1.190 -6.316 3.233 1.00 89.85 4 A 1 ATOM 30 C CA . VAL A 1 4 ? -1.909 -5.252 3.928 1.00 91.08 4 A 1 ATOM 31 C C . VAL A 1 4 ? -1.312 -3.891 3.588 1.00 91.89 4 A 1 ATOM 32 O O . VAL A 1 4 ? -2.035 -2.932 3.302 1.00 90.48 4 A 1 ATOM 33 C CB . VAL A 1 4 ? -1.873 -5.460 5.453 1.00 88.86 4 A 1 ATOM 34 C CG1 . VAL A 1 4 ? -2.625 -4.346 6.162 1.00 82.74 4 A 1 ATOM 35 C CG2 . VAL A 1 4 ? -2.462 -6.814 5.815 1.00 83.30 4 A 1 ATOM 36 N N . PHE A 1 5 ? 0.018 -3.800 3.622 1.00 87.71 5 A 1 ATOM 37 C CA . PHE A 1 5 ? 0.707 -2.561 3.294 1.00 88.41 5 A 1 ATOM 38 C C . PHE A 1 5 ? 0.470 -2.179 1.840 1.00 90.94 5 A 1 ATOM 39 O O . PHE A 1 5 ? 0.385 -0.997 1.503 1.00 89.89 5 A 1 ATOM 40 C CB . PHE A 1 5 ? 2.207 -2.706 3.560 1.00 86.97 5 A 1 ATOM 41 C CG . PHE A 1 5 ? 2.573 -2.483 5.007 1.00 83.08 5 A 1 ATOM 42 C CD1 . PHE A 1 5 ? 2.379 -1.246 5.593 1.00 80.62 5 A 1 ATOM 43 C CD2 . PHE A 1 5 ? 3.114 -3.507 5.763 1.00 79.72 5 A 1 ATOM 44 C CE1 . PHE A 1 5 ? 2.707 -1.028 6.919 1.00 77.17 5 A 1 ATOM 45 C CE2 . PHE A 1 5 ? 3.450 -3.296 7.095 1.00 76.33 5 A 1 ATOM 46 C CZ . PHE A 1 5 ? 3.245 -2.056 7.672 1.00 76.24 5 A 1 ATOM 47 N N . GLY A 1 6 ? 0.366 -3.168 0.981 1.00 90.65 6 A 1 ATOM 48 C CA . GLY A 1 6 ? 0.116 -2.930 -0.434 1.00 91.15 6 A 1 ATOM 49 C C . GLY A 1 6 ? -1.211 -2.237 -0.660 1.00 93.05 6 A 1 ATOM 50 O O . GLY A 1 6 ? -1.326 -1.332 -1.485 1.00 91.65 6 A 1 ATOM 51 N N . ILE A 1 7 ? -2.223 -2.659 0.085 1.00 93.14 7 A 1 ATOM 52 C CA . ILE A 1 7 ? -3.557 -2.077 -0.022 1.00 93.95 7 A 1 ATOM 53 C C . ILE A 1 7 ? -3.574 -0.650 0.517 1.00 94.52 7 A 1 ATOM 54 O O . ILE A 1 7 ? -4.160 0.251 -0.088 1.00 93.15 7 A 1 ATOM 55 C CB . ILE A 1 7 ? -4.590 -2.925 0.745 1.00 93.66 7 A 1 ATOM 56 C CG1 . ILE A 1 7 ? -4.650 -4.338 0.169 1.00 91.09 7 A 1 ATOM 57 C CG2 . ILE A 1 7 ? -5.967 -2.264 0.681 1.00 90.39 7 A 1 ATOM 58 C CD1 . ILE A 1 7 ? -5.431 -5.301 1.034 1.00 84.86 7 A 1 ATOM 59 N N . ILE A 1 8 ? -2.941 -0.448 1.664 1.00 92.69 8 A 1 ATOM 60 C CA . ILE A 1 8 ? -2.887 0.866 2.296 1.00 92.51 8 A 1 ATOM 61 C C . ILE A 1 8 ? -2.121 1.859 1.429 1.00 92.49 8 A 1 ATOM 62 O O . ILE A 1 8 ? -2.593 2.967 1.167 1.00 91.13 8 A 1 ATOM 63 C CB . ILE A 1 8 ? -2.226 0.784 3.684 1.00 91.93 8 A 1 ATOM 64 C CG1 . ILE A 1 8 ? -3.016 -0.145 4.602 1.00 90.06 8 A 1 ATOM 65 C CG2 . ILE A 1 8 ? -2.126 2.180 4.301 1.00 89.00 8 A 1 ATOM 66 C CD1 . ILE A 1 8 ? -2.287 -0.474 5.887 1.00 83.33 8 A 1 ATOM 67 N N . PHE A 1 9 ? -0.932 1.461 0.994 1.00 90.25 9 A 1 ATOM 68 C CA . PHE A 1 9 ? -0.088 2.322 0.173 1.00 89.63 9 A 1 ATOM 69 C C . PHE A 1 9 ? -0.776 2.669 -1.141 1.00 91.13 9 A 1 ATOM 70 O O . PHE A 1 9 ? -0.769 3.820 -1.574 1.00 90.59 9 A 1 ATOM 71 C CB . PHE A 1 9 ? 1.251 1.640 -0.100 1.00 88.50 9 A 1 ATOM 72 C CG . PHE A 1 9 ? 2.360 2.621 -0.384 1.00 85.80 9 A 1 ATOM 73 C CD1 . PHE A 1 9 ? 2.924 3.355 0.643 1.00 84.01 9 A 1 ATOM 74 C CD2 . PHE A 1 9 ? 2.825 2.800 -1.673 1.00 83.83 9 A 1 ATOM 75 C CE1 . PHE A 1 9 ? 3.940 4.261 0.392 1.00 82.00 9 A 1 ATOM 76 C CE2 . PHE A 1 9 ? 3.844 3.709 -1.936 1.00 82.64 9 A 1 ATOM 77 C CZ . PHE A 1 9 ? 4.403 4.439 -0.904 1.00 82.31 9 A 1 ATOM 78 N N . THR A 1 10 ? -1.378 1.675 -1.765 1.00 92.14 10 A 1 ATOM 79 C CA . THR A 1 10 ? -2.077 1.884 -3.032 1.00 91.88 10 A 1 ATOM 80 C C . THR A 1 10 ? -3.291 2.788 -2.835 1.00 92.63 10 A 1 ATOM 81 O O . THR A 1 10 ? -3.564 3.664 -3.657 1.00 90.66 10 A 1 ATOM 82 C CB . THR A 1 10 ? -2.541 0.550 -3.629 1.00 90.28 10 A 1 ATOM 83 O OG1 . THR A 1 10 ? -1.425 -0.315 -3.795 1.00 82.65 10 A 1 ATOM 84 C CG2 . THR A 1 10 ? -3.201 0.767 -4.982 1.00 82.74 10 A 1 ATOM 85 N N . SER A 1 11 ? -4.021 2.585 -1.743 1.00 91.35 11 A 1 ATOM 86 C CA . SER A 1 11 ? -5.207 3.374 -1.437 1.00 91.55 11 A 1 ATOM 87 C C . SER A 1 11 ? -4.850 4.834 -1.199 1.00 92.61 11 A 1 ATOM 88 O O . SER A 1 11 ? -5.564 5.735 -1.632 1.00 90.83 11 A 1 ATOM 89 C CB . SER A 1 11 ? -5.917 2.817 -0.207 1.00 90.59 11 A 1 ATOM 90 O OG . SER A 1 11 ? -7.103 3.529 0.040 1.00 83.38 11 A 1 ATOM 91 N N . VAL A 1 12 ? -3.737 5.073 -0.503 1.00 93.51 12 A 1 ATOM 92 C CA . VAL A 1 12 ? -3.282 6.431 -0.209 1.00 93.74 12 A 1 ATOM 93 C C . VAL A 1 12 ? -2.939 7.184 -1.488 1.00 94.58 12 A 1 ATOM 94 O O . VAL A 1 12 ? -3.312 8.346 -1.655 1.00 93.50 12 A 1 ATOM 95 C CB . VAL A 1 12 ? -2.058 6.413 0.721 1.00 92.06 12 A 1 ATOM 96 C CG1 . VAL A 1 12 ? -1.497 7.817 0.897 1.00 87.62 12 A 1 ATOM 97 C CG2 . VAL A 1 12 ? -2.433 5.833 2.072 1.00 87.76 12 A 1 ATOM 98 N N . ILE A 1 13 ? -2.222 6.529 -2.379 1.00 94.98 13 A 1 ATOM 99 C CA . ILE A 1 13 ? -1.815 7.148 -3.637 1.00 94.66 13 A 1 ATOM 100 C C . ILE A 1 13 ? -3.003 7.341 -4.572 1.00 94.57 13 A 1 ATOM 101 O O . ILE A 1 13 ? -3.156 8.392 -5.198 1.00 93.65 13 A 1 ATOM 102 C CB . ILE A 1 13 ? -0.740 6.304 -4.339 1.00 93.81 13 A 1 ATOM 103 C CG1 . ILE A 1 13 ? 0.486 6.129 -3.430 1.00 91.85 13 A 1 ATOM 104 C CG2 . ILE A 1 13 ? -0.328 6.958 -5.656 1.00 90.99 13 A 1 ATOM 105 C CD1 . ILE A 1 13 ? 1.138 7.440 -3.041 1.00 85.73 13 A 1 ATOM 106 N N . VAL A 1 14 ? -3.841 6.322 -4.674 1.00 94.69 14 A 1 ATOM 107 C CA . VAL A 1 14 ? -5.009 6.367 -5.548 1.00 94.00 14 A 1 ATOM 108 C C . VAL A 1 14 ? -6.047 7.358 -5.037 1.00 93.57 14 A 1 ATOM 109 O O . VAL A 1 14 ? -6.529 8.214 -5.787 1.00 91.63 14 A 1 ATOM 110 C CB . VAL A 1 14 ? -5.648 4.976 -5.682 1.00 91.79 14 A 1 ATOM 111 C CG1 . VAL A 1 14 ? -6.939 5.063 -6.489 1.00 86.82 14 A 1 ATOM 112 C CG2 . VAL A 1 14 ? -4.684 4.012 -6.342 1.00 87.36 14 A 1 ATOM 113 N N . THR A 1 15 ? -6.390 7.234 -3.759 1.00 93.69 15 A 1 ATOM 114 C CA . THR A 1 15 ? -7.382 8.117 -3.147 1.00 92.07 15 A 1 ATOM 115 C C . THR A 1 15 ? -6.702 9.237 -2.372 1.00 91.30 15 A 1 ATOM 116 O O . THR A 1 15 ? -7.111 9.576 -1.254 1.00 87.33 15 A 1 ATOM 117 C CB . THR A 1 15 ? -8.305 7.330 -2.205 1.00 89.23 15 A 1 ATOM 118 O OG1 . THR A 1 15 ? -7.553 6.757 -1.141 1.00 84.34 15 A 1 ATOM 119 C CG2 . THR A 1 15 ? -9.026 6.230 -2.966 1.00 82.87 15 A 1 ATOM 120 N N . SER A 1 16 ? -5.670 9.810 -2.986 1.00 92.41 16 A 1 ATOM 121 C CA . SER A 1 16 ? -4.912 10.885 -2.349 1.00 90.75 16 A 1 ATOM 122 C C . SER A 1 16 ? -5.729 12.179 -2.321 1.00 88.42 16 A 1 ATOM 123 O O . SER A 1 16 ? -6.540 12.350 -1.386 1.00 84.25 16 A 1 ATOM 124 C CB . SER A 1 16 ? -3.596 11.118 -3.082 1.00 86.41 16 A 1 ATOM 125 O OG . SER A 1 16 ? -2.846 12.125 -2.440 1.00 79.34 16 A 1 ATOM 126 O OXT . SER A 1 16 ? -5.574 12.994 -3.219 1.00 80.19 16 A 1 #