# 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_spkb09729 # _entry.id spkb09729 # 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 "C5 H9 N O4" 147.129 GLU y "GLUTAMIC ACID" C(CC(=O)O)[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" "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" "C9 H11 N O3" 181.189 TYR y TYROSINE c1cc(ccc1C[C@@H](C(=O)O)N)O ? "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 LEU 2 1 n THR 3 1 n TRP 4 1 n PHE 5 1 n LEU 6 1 n PHE 7 1 n TYR 8 1 n PHE 9 1 n SER 10 1 n GLU 11 # _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 @ 2025-07-09 00:57:27)" _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 88.46 _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 82.43 1 1 A LEU 2 2 87.59 1 2 A THR 3 2 91.27 1 3 A TRP 4 2 90.58 1 4 A PHE 5 2 92.04 1 5 A LEU 6 2 92.25 1 6 A PHE 7 2 90.51 1 7 A TYR 8 2 89.40 1 8 A PHE 9 2 87.42 1 9 A SER 10 2 88.00 1 10 A GLU 11 2 80.07 1 11 # _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 LEU . 2 A 2 A 3 1 n THR . 3 A 3 A 4 1 n TRP . 4 A 4 A 5 1 n PHE . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n PHE . 7 A 7 A 8 1 n TYR . 8 A 8 A 9 1 n PHE . 9 A 9 A 10 1 n SER . 10 A 10 A 11 1 n GLU . 11 A 11 # _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 ? 7.692 -1.165 5.687 1.00 86.33 1 A 1 ATOM 2 C CA . MET A 1 1 ? 7.604 -0.445 4.402 1.00 88.83 1 A 1 ATOM 3 C C . MET A 1 1 ? 6.157 -0.018 4.144 1.00 90.51 1 A 1 ATOM 4 O O . MET A 1 1 ? 5.289 -0.860 3.920 1.00 88.89 1 A 1 ATOM 5 C CB . MET A 1 1 ? 8.106 -1.330 3.265 1.00 84.13 1 A 1 ATOM 6 C CG . MET A 1 1 ? 9.634 -1.446 3.217 1.00 78.28 1 A 1 ATOM 7 S SD . MET A 1 1 ? 10.343 -2.120 4.722 1.00 75.02 1 A 1 ATOM 8 C CE . MET A 1 1 ? 12.084 -1.977 4.350 1.00 67.48 1 A 1 ATOM 9 N N . LEU A 1 2 ? 5.923 1.288 4.178 1.00 86.26 2 A 1 ATOM 10 C CA . LEU A 1 2 ? 4.592 1.863 3.995 1.00 90.51 2 A 1 ATOM 11 C C . LEU A 1 2 ? 4.131 1.779 2.538 1.00 93.34 2 A 1 ATOM 12 O O . LEU A 1 2 ? 2.942 1.890 2.251 1.00 92.26 2 A 1 ATOM 13 C CB . LEU A 1 2 ? 4.605 3.318 4.482 1.00 89.71 2 A 1 ATOM 14 C CG . LEU A 1 2 ? 3.353 3.745 5.249 1.00 85.09 2 A 1 ATOM 15 C CD1 . LEU A 1 2 ? 3.684 4.895 6.191 1.00 82.02 2 A 1 ATOM 16 C CD2 . LEU A 1 2 ? 2.238 4.146 4.308 1.00 81.54 2 A 1 ATOM 17 N N . THR A 1 3 ? 5.061 1.564 1.639 1.00 92.43 3 A 1 ATOM 18 C CA . THR A 1 3 ? 4.772 1.460 0.211 1.00 94.33 3 A 1 ATOM 19 C C . THR A 1 3 ? 3.793 0.320 -0.075 1.00 94.77 3 A 1 ATOM 20 O O . THR A 1 3 ? 2.991 0.399 -1.007 1.00 93.46 3 A 1 ATOM 21 C CB . THR A 1 3 ? 6.068 1.245 -0.586 1.00 93.07 3 A 1 ATOM 22 O OG1 . THR A 1 3 ? 7.097 2.112 -0.108 1.00 85.56 3 A 1 ATOM 23 C CG2 . THR A 1 3 ? 5.844 1.515 -2.067 1.00 85.25 3 A 1 ATOM 24 N N . TRP A 1 4 ? 3.841 -0.724 0.741 1.00 94.65 4 A 1 ATOM 25 C CA . TRP A 1 4 ? 2.956 -1.868 0.592 1.00 95.22 4 A 1 ATOM 26 C C . TRP A 1 4 ? 1.507 -1.490 0.883 1.00 95.58 4 A 1 ATOM 27 O O . TRP A 1 4 ? 0.591 -1.997 0.239 1.00 94.27 4 A 1 ATOM 28 C CB . TRP A 1 4 ? 3.410 -3.005 1.504 1.00 95.00 4 A 1 ATOM 29 C CG . TRP A 1 4 ? 3.958 -4.176 0.753 1.00 92.62 4 A 1 ATOM 30 C CD1 . TRP A 1 4 ? 5.228 -4.317 0.287 1.00 89.14 4 A 1 ATOM 31 C CD2 . TRP A 1 4 ? 3.259 -5.365 0.371 1.00 91.00 4 A 1 ATOM 32 N NE1 . TRP A 1 4 ? 5.359 -5.522 -0.366 1.00 86.57 4 A 1 ATOM 33 C CE2 . TRP A 1 4 ? 4.164 -6.198 -0.333 1.00 89.97 4 A 1 ATOM 34 C CE3 . TRP A 1 4 ? 1.944 -5.819 0.546 1.00 87.11 4 A 1 ATOM 35 C CZ2 . TRP A 1 4 ? 3.793 -7.434 -0.845 1.00 88.92 4 A 1 ATOM 36 C CZ3 . TRP A 1 4 ? 1.578 -7.052 0.039 1.00 84.02 4 A 1 ATOM 37 C CH2 . TRP A 1 4 ? 2.496 -7.846 -0.655 1.00 84.08 4 A 1 ATOM 38 N N . PHE A 1 5 ? 1.316 -0.582 1.829 1.00 94.79 5 A 1 ATOM 39 C CA . PHE A 1 5 ? -0.015 -0.120 2.190 1.00 95.10 5 A 1 ATOM 40 C C . PHE A 1 5 ? -0.625 0.718 1.070 1.00 95.75 5 A 1 ATOM 41 O O . PHE A 1 5 ? -1.825 0.635 0.806 1.00 94.97 5 A 1 ATOM 42 C CB . PHE A 1 5 ? 0.033 0.693 3.485 1.00 94.88 5 A 1 ATOM 43 C CG . PHE A 1 5 ? 0.231 -0.148 4.724 1.00 93.63 5 A 1 ATOM 44 C CD1 . PHE A 1 5 ? -0.784 -0.967 5.184 1.00 89.59 5 A 1 ATOM 45 C CD2 . PHE A 1 5 ? 1.427 -0.100 5.418 1.00 90.10 5 A 1 ATOM 46 C CE1 . PHE A 1 5 ? -0.611 -1.739 6.320 1.00 87.99 5 A 1 ATOM 47 C CE2 . PHE A 1 5 ? 1.602 -0.874 6.558 1.00 87.67 5 A 1 ATOM 48 C CZ . PHE A 1 5 ? 0.586 -1.694 7.004 1.00 87.98 5 A 1 ATOM 49 N N . LEU A 1 6 ? 0.192 1.514 0.434 1.00 94.96 6 A 1 ATOM 50 C CA . LEU A 1 6 ? -0.258 2.354 -0.670 1.00 95.27 6 A 1 ATOM 51 C C . LEU A 1 6 ? -0.702 1.501 -1.857 1.00 95.55 6 A 1 ATOM 52 O O . LEU A 1 6 ? -1.704 1.801 -2.506 1.00 95.05 6 A 1 ATOM 53 C CB . LEU A 1 6 ? 0.865 3.302 -1.102 1.00 95.09 6 A 1 ATOM 54 C CG . LEU A 1 6 ? 1.258 4.352 -0.071 1.00 89.51 6 A 1 ATOM 55 C CD1 . LEU A 1 6 ? 2.565 5.023 -0.469 1.00 85.94 6 A 1 ATOM 56 C CD2 . LEU A 1 6 ? 0.163 5.399 0.075 1.00 86.61 6 A 1 ATOM 57 N N . PHE A 1 7 ? 0.041 0.451 -2.122 1.00 94.52 7 A 1 ATOM 58 C CA . PHE A 1 7 ? -0.273 -0.469 -3.208 1.00 94.37 7 A 1 ATOM 59 C C . PHE A 1 7 ? -1.529 -1.280 -2.897 1.00 94.54 7 A 1 ATOM 60 O O . PHE A 1 7 ? -2.335 -1.547 -3.788 1.00 93.28 7 A 1 ATOM 61 C CB . PHE A 1 7 ? 0.918 -1.401 -3.452 1.00 93.73 7 A 1 ATOM 62 C CG . PHE A 1 7 ? 0.720 -2.336 -4.617 1.00 91.65 7 A 1 ATOM 63 C CD1 . PHE A 1 7 ? 0.812 -1.866 -5.918 1.00 88.08 7 A 1 ATOM 64 C CD2 . PHE A 1 7 ? 0.441 -3.671 -4.401 1.00 87.51 7 A 1 ATOM 65 C CE1 . PHE A 1 7 ? 0.626 -2.716 -6.996 1.00 86.09 7 A 1 ATOM 66 C CE2 . PHE A 1 7 ? 0.249 -4.528 -5.480 1.00 86.23 7 A 1 ATOM 67 C CZ . PHE A 1 7 ? 0.343 -4.049 -6.773 1.00 85.58 7 A 1 ATOM 68 N N . TYR A 1 8 ? -1.686 -1.650 -1.644 1.00 92.22 8 A 1 ATOM 69 C CA . TYR A 1 8 ? -2.844 -2.419 -1.191 1.00 92.68 8 A 1 ATOM 70 C C . TYR A 1 8 ? -4.123 -1.589 -1.248 1.00 93.26 8 A 1 ATOM 71 O O . TYR A 1 8 ? -5.191 -2.093 -1.596 1.00 92.36 8 A 1 ATOM 72 C CB . TYR A 1 8 ? -2.602 -2.922 0.234 1.00 92.37 8 A 1 ATOM 73 C CG . TYR A 1 8 ? -3.738 -3.766 0.768 1.00 90.14 8 A 1 ATOM 74 C CD1 . TYR A 1 8 ? -3.889 -5.089 0.364 1.00 87.95 8 A 1 ATOM 75 C CD2 . TYR A 1 8 ? -4.653 -3.236 1.666 1.00 87.08 8 A 1 ATOM 76 C CE1 . TYR A 1 8 ? -4.934 -5.863 0.847 1.00 86.17 8 A 1 ATOM 77 C CE2 . TYR A 1 8 ? -5.708 -4.005 2.153 1.00 86.87 8 A 1 ATOM 78 C CZ . TYR A 1 8 ? -5.839 -5.317 1.740 1.00 86.59 8 A 1 ATOM 79 O OH . TYR A 1 8 ? -6.876 -6.077 2.218 1.00 85.07 8 A 1 ATOM 80 N N . PHE A 1 9 ? -4.013 -0.311 -0.896 1.00 89.92 9 A 1 ATOM 81 C CA . PHE A 1 9 ? -5.153 0.598 -0.895 1.00 90.13 9 A 1 ATOM 82 C C . PHE A 1 9 ? -5.527 1.018 -2.315 1.00 91.42 9 A 1 ATOM 83 O O . PHE A 1 9 ? -6.668 1.398 -2.572 1.00 90.98 9 A 1 ATOM 84 C CB . PHE A 1 9 ? -4.839 1.834 -0.036 1.00 89.28 9 A 1 ATOM 85 C CG . PHE A 1 9 ? -6.065 2.572 0.438 1.00 88.53 9 A 1 ATOM 86 C CD1 . PHE A 1 9 ? -6.987 1.948 1.255 1.00 85.31 9 A 1 ATOM 87 C CD2 . PHE A 1 9 ? -6.284 3.887 0.062 1.00 84.46 9 A 1 ATOM 88 C CE1 . PHE A 1 9 ? -8.118 2.618 1.695 1.00 83.66 9 A 1 ATOM 89 C CE2 . PHE A 1 9 ? -7.415 4.565 0.498 1.00 83.99 9 A 1 ATOM 90 C CZ . PHE A 1 9 ? -8.331 3.930 1.315 1.00 83.92 9 A 1 ATOM 91 N N . SER A 1 10 ? -4.568 0.960 -3.210 1.00 91.60 10 A 1 ATOM 92 C CA . SER A 1 10 ? -4.791 1.322 -4.603 1.00 90.39 10 A 1 ATOM 93 C C . SER A 1 10 ? -5.529 0.216 -5.347 1.00 89.70 10 A 1 ATOM 94 O O . SER A 1 10 ? -6.377 0.486 -6.198 1.00 87.32 10 A 1 ATOM 95 C CB . SER A 1 10 ? -3.460 1.621 -5.297 1.00 87.58 10 A 1 ATOM 96 O OG . SER A 1 10 ? -3.676 2.283 -6.521 1.00 81.41 10 A 1 ATOM 97 N N . GLU A 1 11 ? -5.196 -0.996 -5.027 1.00 88.70 11 A 1 ATOM 98 C CA . GLU A 1 11 ? -5.808 -2.169 -5.654 1.00 86.13 11 A 1 ATOM 99 C C . GLU A 1 11 ? -7.125 -2.543 -4.954 1.00 81.92 11 A 1 ATOM 100 O O . GLU A 1 11 ? -8.160 -1.912 -5.280 1.00 79.62 11 A 1 ATOM 101 C CB . GLU A 1 11 ? -4.824 -3.347 -5.632 1.00 81.07 11 A 1 ATOM 102 C CG . GLU A 1 11 ? -5.274 -4.534 -6.466 1.00 79.48 11 A 1 ATOM 103 C CD . GLU A 1 11 ? -5.188 -4.266 -7.955 1.00 77.83 11 A 1 ATOM 104 O OE1 . GLU A 1 11 ? -4.288 -3.538 -8.385 1.00 72.80 11 A 1 ATOM 105 O OE2 . GLU A 1 11 ? -6.047 -4.800 -8.688 1.00 73.78 11 A 1 ATOM 106 O OXT . GLU A 1 11 ? -7.159 -3.442 -4.130 1.00 79.37 11 A 1 #