# 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_spkb22902 # _entry.id spkb22902 # 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 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" "C5 H9 N O2" 115.130 PRO y PROLINE C1C[C@H](NC1)C(=O)O ? "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" # _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 PHE 3 1 n THR 4 1 n ALA 5 1 n SER 6 1 n LEU 7 1 n LEU 8 1 n LEU 9 1 n LEU 10 1 n LEU 11 1 n PRO 12 1 n TRP 13 1 n ALA 14 1 n SER 15 1 n ALA 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 @ 2025-07-09 13:13:27)" _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 88.51 _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 78.58 1 1 A LEU 2 2 84.09 1 2 A PHE 3 2 86.41 1 3 A THR 4 2 90.75 1 4 A ALA 5 2 93.63 1 5 A SER 6 2 92.45 1 6 A LEU 7 2 90.50 1 7 A LEU 8 2 90.92 1 8 A LEU 9 2 90.80 1 9 A LEU 10 2 92.65 1 10 A LEU 11 2 89.79 1 11 A PRO 12 2 93.91 1 12 A TRP 13 2 85.08 1 13 A ALA 14 2 93.60 1 14 A SER 15 2 88.58 1 15 A ALA 16 2 81.91 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 LEU . 2 A 2 A 3 1 n PHE . 3 A 3 A 4 1 n THR . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n SER . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n PRO . 12 A 12 A 13 1 n TRP . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n SER . 15 A 15 A 16 1 n ALA . 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 ? -11.833 1.861 5.214 1.00 82.48 1 A 1 ATOM 2 C CA . MET A 1 1 ? -10.465 1.328 5.161 1.00 84.52 1 A 1 ATOM 3 C C . MET A 1 1 ? -9.601 2.061 4.128 1.00 86.56 1 A 1 ATOM 4 O O . MET A 1 1 ? -8.787 1.449 3.439 1.00 85.78 1 A 1 ATOM 5 C CB . MET A 1 1 ? -10.498 -0.164 4.825 1.00 79.83 1 A 1 ATOM 6 C CG . MET A 1 1 ? -11.062 -1.013 5.941 1.00 75.06 1 A 1 ATOM 7 S SD . MET A 1 1 ? -11.125 -2.750 5.476 1.00 71.60 1 A 1 ATOM 8 C CE . MET A 1 1 ? -11.582 -3.475 7.039 1.00 62.79 1 A 1 ATOM 9 N N . LEU A 1 2 ? -9.790 3.360 4.036 1.00 84.19 2 A 1 ATOM 10 C CA . LEU A 1 2 ? -9.031 4.177 3.088 1.00 87.73 2 A 1 ATOM 11 C C . LEU A 1 2 ? -7.586 4.356 3.540 1.00 90.99 2 A 1 ATOM 12 O O . LEU A 1 2 ? -6.659 4.276 2.733 1.00 89.74 2 A 1 ATOM 13 C CB . LEU A 1 2 ? -9.710 5.543 2.919 1.00 85.81 2 A 1 ATOM 14 C CG . LEU A 1 2 ? -10.402 5.756 1.585 1.00 81.98 2 A 1 ATOM 15 C CD1 . LEU A 1 2 ? -11.388 6.913 1.678 1.00 77.55 2 A 1 ATOM 16 C CD2 . LEU A 1 2 ? -9.381 6.020 0.492 1.00 74.71 2 A 1 ATOM 17 N N . PHE A 1 3 ? -7.396 4.579 4.834 1.00 87.01 3 A 1 ATOM 18 C CA . PHE A 1 3 ? -6.067 4.769 5.403 1.00 88.98 3 A 1 ATOM 19 C C . PHE A 1 3 ? -5.223 3.506 5.278 1.00 92.43 3 A 1 ATOM 20 O O . PHE A 1 3 ? -4.020 3.583 5.014 1.00 92.31 3 A 1 ATOM 21 C CB . PHE A 1 3 ? -6.190 5.181 6.869 1.00 87.83 3 A 1 ATOM 22 C CG . PHE A 1 3 ? -4.946 5.825 7.404 1.00 86.35 3 A 1 ATOM 23 C CD1 . PHE A 1 3 ? -4.644 7.139 7.092 1.00 83.47 3 A 1 ATOM 24 C CD2 . PHE A 1 3 ? -4.086 5.112 8.214 1.00 83.71 3 A 1 ATOM 25 C CE1 . PHE A 1 3 ? -3.500 7.741 7.580 1.00 83.02 3 A 1 ATOM 26 C CE2 . PHE A 1 3 ? -2.933 5.708 8.704 1.00 82.32 3 A 1 ATOM 27 C CZ . PHE A 1 3 ? -2.639 7.021 8.388 1.00 83.07 3 A 1 ATOM 28 N N . THR A 1 4 ? -5.863 2.364 5.461 1.00 92.12 4 A 1 ATOM 29 C CA . THR A 1 4 ? -5.184 1.072 5.360 1.00 93.01 4 A 1 ATOM 30 C C . THR A 1 4 ? -4.672 0.838 3.942 1.00 93.01 4 A 1 ATOM 31 O O . THR A 1 4 ? -3.554 0.354 3.750 1.00 92.36 4 A 1 ATOM 32 C CB . THR A 1 4 ? -6.118 -0.078 5.760 1.00 92.18 4 A 1 ATOM 33 O OG1 . THR A 1 4 ? -6.877 0.292 6.909 1.00 87.14 4 A 1 ATOM 34 C CG2 . THR A 1 4 ? -5.327 -1.335 6.075 1.00 85.44 4 A 1 ATOM 35 N N . ALA A 1 5 ? -5.488 1.175 2.960 1.00 94.49 5 A 1 ATOM 36 C CA . ALA A 1 5 ? -5.128 1.004 1.557 1.00 93.78 5 A 1 ATOM 37 C C . ALA A 1 5 ? -3.954 1.900 1.173 1.00 94.26 5 A 1 ATOM 38 O O . ALA A 1 5 ? -3.050 1.473 0.452 1.00 92.95 5 A 1 ATOM 39 C CB . ALA A 1 5 ? -6.332 1.298 0.672 1.00 92.67 5 A 1 ATOM 40 N N . SER A 1 6 ? -3.959 3.115 1.676 1.00 94.21 6 A 1 ATOM 41 C CA . SER A 1 6 ? -2.902 4.082 1.400 1.00 93.61 6 A 1 ATOM 42 C C . SER A 1 6 ? -1.578 3.640 2.012 1.00 94.03 6 A 1 ATOM 43 O O . SER A 1 6 ? -0.522 3.782 1.396 1.00 92.61 6 A 1 ATOM 44 C CB . SER A 1 6 ? -3.289 5.452 1.936 1.00 92.95 6 A 1 ATOM 45 O OG . SER A 1 6 ? -4.425 5.951 1.271 1.00 87.30 6 A 1 ATOM 46 N N . LEU A 1 7 ? -1.657 3.094 3.215 1.00 92.45 7 A 1 ATOM 47 C CA . LEU A 1 7 ? -0.474 2.614 3.921 1.00 92.56 7 A 1 ATOM 48 C C . LEU A 1 7 ? 0.143 1.413 3.216 1.00 93.81 7 A 1 ATOM 49 O O . LEU A 1 7 ? 1.364 1.314 3.097 1.00 93.35 7 A 1 ATOM 50 C CB . LEU A 1 7 ? -0.837 2.239 5.359 1.00 92.42 7 A 1 ATOM 51 C CG . LEU A 1 7 ? 0.249 2.541 6.379 1.00 88.54 7 A 1 ATOM 52 C CD1 . LEU A 1 7 ? -0.058 3.834 7.124 1.00 85.67 7 A 1 ATOM 53 C CD2 . LEU A 1 7 ? 0.397 1.393 7.354 1.00 85.20 7 A 1 ATOM 54 N N . LEU A 1 8 ? -0.710 0.506 2.754 1.00 92.71 8 A 1 ATOM 55 C CA . LEU A 1 8 ? -0.260 -0.694 2.058 1.00 92.51 8 A 1 ATOM 56 C C . LEU A 1 8 ? 0.401 -0.355 0.728 1.00 93.75 8 A 1 ATOM 57 O O . LEU A 1 8 ? 1.355 -1.020 0.318 1.00 93.68 8 A 1 ATOM 58 C CB . LEU A 1 8 ? -1.443 -1.641 1.825 1.00 92.65 8 A 1 ATOM 59 C CG . LEU A 1 8 ? -1.888 -2.437 3.047 1.00 89.36 8 A 1 ATOM 60 C CD1 . LEU A 1 8 ? -3.319 -2.917 2.886 1.00 86.75 8 A 1 ATOM 61 C CD2 . LEU A 1 8 ? -0.961 -3.623 3.281 1.00 85.98 8 A 1 ATOM 62 N N . LEU A 1 9 ? -0.102 0.666 0.065 1.00 92.02 9 A 1 ATOM 63 C CA . LEU A 1 9 ? 0.434 1.095 -1.220 1.00 91.71 9 A 1 ATOM 64 C C . LEU A 1 9 ? 1.738 1.874 -1.055 1.00 93.28 9 A 1 ATOM 65 O O . LEU A 1 9 ? 2.631 1.775 -1.902 1.00 92.28 9 A 1 ATOM 66 C CB . LEU A 1 9 ? -0.598 1.953 -1.956 1.00 91.83 9 A 1 ATOM 67 C CG . LEU A 1 9 ? -1.776 1.190 -2.553 1.00 89.97 9 A 1 ATOM 68 C CD1 . LEU A 1 9 ? -2.952 2.123 -2.796 1.00 87.77 9 A 1 ATOM 69 C CD2 . LEU A 1 9 ? -1.370 0.509 -3.851 1.00 87.54 9 A 1 ATOM 70 N N . LEU A 1 10 ? 1.847 2.621 0.029 1.00 93.62 10 A 1 ATOM 71 C CA . LEU A 1 10 ? 3.033 3.426 0.300 1.00 93.60 10 A 1 ATOM 72 C C . LEU A 1 10 ? 4.157 2.608 0.926 1.00 94.56 10 A 1 ATOM 73 O O . LEU A 1 10 ? 5.331 2.950 0.758 1.00 93.49 10 A 1 ATOM 74 C CB . LEU A 1 10 ? 2.671 4.594 1.222 1.00 93.74 10 A 1 ATOM 75 C CG . LEU A 1 10 ? 1.860 5.711 0.575 1.00 92.32 10 A 1 ATOM 76 C CD1 . LEU A 1 10 ? 1.156 6.541 1.632 1.00 90.21 10 A 1 ATOM 77 C CD2 . LEU A 1 10 ? 2.765 6.596 -0.270 1.00 89.63 10 A 1 ATOM 78 N N . LEU A 1 11 ? 3.796 1.547 1.624 1.00 92.43 11 A 1 ATOM 79 C CA . LEU A 1 11 ? 4.773 0.678 2.285 1.00 91.83 11 A 1 ATOM 80 C C . LEU A 1 11 ? 5.812 0.123 1.308 1.00 92.45 11 A 1 ATOM 81 O O . LEU A 1 11 ? 7.015 0.302 1.532 1.00 91.46 11 A 1 ATOM 82 C CB . LEU A 1 11 ? 4.046 -0.460 3.017 1.00 91.27 11 A 1 ATOM 83 C CG . LEU A 1 11 ? 4.913 -1.301 3.952 1.00 88.55 11 A 1 ATOM 84 C CD1 . LEU A 1 11 ? 5.240 -0.529 5.228 1.00 85.63 11 A 1 ATOM 85 C CD2 . LEU A 1 11 ? 4.207 -2.596 4.295 1.00 84.70 11 A 1 ATOM 86 N N . PRO A 1 12 ? 5.384 -0.560 0.237 1.00 95.31 12 A 1 ATOM 87 C CA . PRO A 1 12 ? 6.335 -1.111 -0.737 1.00 94.59 12 A 1 ATOM 88 C C . PRO A 1 12 ? 7.080 -0.026 -1.500 1.00 94.84 12 A 1 ATOM 89 O O . PRO A 1 12 ? 8.248 -0.202 -1.857 1.00 92.96 12 A 1 ATOM 90 C CB . PRO A 1 12 ? 5.445 -1.928 -1.683 1.00 93.03 12 A 1 ATOM 91 C CG . PRO A 1 12 ? 4.102 -1.326 -1.551 1.00 92.53 12 A 1 ATOM 92 C CD . PRO A 1 12 ? 4.003 -0.823 -0.131 1.00 94.13 12 A 1 ATOM 93 N N . TRP A 1 13 ? 6.421 1.073 -1.742 1.00 90.84 13 A 1 ATOM 94 C CA . TRP A 1 13 ? 7.018 2.198 -2.451 1.00 90.58 13 A 1 ATOM 95 C C . TRP A 1 13 ? 8.102 2.867 -1.614 1.00 91.01 13 A 1 ATOM 96 O O . TRP A 1 13 ? 9.170 3.199 -2.130 1.00 88.61 13 A 1 ATOM 97 C CB . TRP A 1 13 ? 5.937 3.218 -2.817 1.00 88.90 13 A 1 ATOM 98 C CG . TRP A 1 13 ? 6.398 4.233 -3.806 1.00 85.87 13 A 1 ATOM 99 C CD1 . TRP A 1 13 ? 6.430 4.092 -5.159 1.00 83.30 13 A 1 ATOM 100 C CD2 . TRP A 1 13 ? 6.896 5.555 -3.530 1.00 86.00 13 A 1 ATOM 101 N NE1 . TRP A 1 13 ? 6.916 5.241 -5.744 1.00 81.60 13 A 1 ATOM 102 C CE2 . TRP A 1 13 ? 7.211 6.157 -4.775 1.00 83.96 13 A 1 ATOM 103 C CE3 . TRP A 1 13 ? 7.110 6.290 -2.363 1.00 81.48 13 A 1 ATOM 104 C CZ2 . TRP A 1 13 ? 7.723 7.450 -4.866 1.00 81.73 13 A 1 ATOM 105 C CZ3 . TRP A 1 13 ? 7.621 7.575 -2.455 1.00 78.38 13 A 1 ATOM 106 C CH2 . TRP A 1 13 ? 7.923 8.148 -3.699 1.00 78.90 13 A 1 ATOM 107 N N . ALA A 1 14 ? 7.828 3.051 -0.335 1.00 94.40 14 A 1 ATOM 108 C CA . ALA A 1 14 ? 8.774 3.668 0.588 1.00 93.90 14 A 1 ATOM 109 C C . ALA A 1 14 ? 9.934 2.737 0.924 1.00 94.28 14 A 1 ATOM 110 O O . ALA A 1 14 ? 11.046 3.195 1.186 1.00 93.01 14 A 1 ATOM 111 C CB . ALA A 1 14 ? 8.056 4.093 1.865 1.00 92.40 14 A 1 ATOM 112 N N . SER A 1 15 ? 9.668 1.435 0.924 1.00 92.86 15 A 1 ATOM 113 C CA . SER A 1 15 ? 10.676 0.426 1.230 1.00 91.53 15 A 1 ATOM 114 C C . SER A 1 15 ? 11.780 0.409 0.182 1.00 90.30 15 A 1 ATOM 115 O O . SER A 1 15 ? 12.951 0.190 0.506 1.00 86.69 15 A 1 ATOM 116 C CB . SER A 1 15 ? 10.034 -0.952 1.329 1.00 89.24 15 A 1 ATOM 117 O OG . SER A 1 15 ? 10.906 -1.867 1.937 1.00 80.87 15 A 1 ATOM 118 N N . ALA A 1 16 ? 11.409 0.643 -1.070 1.00 88.87 16 A 1 ATOM 119 C CA . ALA A 1 16 ? 12.344 0.658 -2.189 1.00 86.16 16 A 1 ATOM 120 C C . ALA A 1 16 ? 13.135 1.959 -2.214 1.00 83.45 16 A 1 ATOM 121 O O . ALA A 1 16 ? 14.267 1.990 -1.698 1.00 79.02 16 A 1 ATOM 122 C CB . ALA A 1 16 ? 11.595 0.457 -3.499 1.00 79.98 16 A 1 ATOM 123 O OXT . ALA A 1 16 ? 12.619 2.954 -2.714 1.00 73.97 16 A 1 #