# 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_spkb10172 # _entry.id spkb10172 # 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" "C2 H5 N O2" 75.067 GLY y GLYCINE C(C(=O)O)N ? "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" "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" "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 TRP 2 1 n THR 3 1 n LEU 4 1 n VAL 5 1 n SER 6 1 n TRP 7 1 n VAL 8 1 n ALA 9 1 n LEU 10 1 n THR 11 1 n ALA 12 1 n GLY 13 1 n LEU 14 1 n VAL 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 @ 2025-07-04 01:04:34)" _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 95.52 _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 91.12 1 1 A TRP 2 2 91.39 1 2 A THR 3 2 96.79 1 3 A LEU 4 2 96.31 1 4 A VAL 5 2 97.13 1 5 A SER 6 2 97.39 1 6 A TRP 7 2 95.97 1 7 A VAL 8 2 97.56 1 8 A ALA 9 2 97.69 1 9 A LEU 10 2 95.37 1 10 A THR 11 2 96.95 1 11 A ALA 12 2 97.90 1 12 A GLY 13 2 98.14 1 13 A LEU 14 2 96.19 1 14 A VAL 15 2 97.33 1 15 A ALA 16 2 96.42 1 16 A GLY 17 2 89.47 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 TRP . 2 A 2 A 3 1 n THR . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n SER . 6 A 6 A 7 1 n TRP . 7 A 7 A 8 1 n VAL . 8 A 8 A 9 1 n ALA . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n THR . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n GLY . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n VAL . 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 ? -5.796 6.152 8.373 1.00 94.46 1 A 1 ATOM 2 C CA . MET A 1 1 ? -4.767 5.115 8.149 1.00 95.43 1 A 1 ATOM 3 C C . MET A 1 1 ? -3.967 5.432 6.885 1.00 96.09 1 A 1 ATOM 4 O O . MET A 1 1 ? -4.448 5.223 5.772 1.00 94.97 1 A 1 ATOM 5 C CB . MET A 1 1 ? -5.422 3.745 7.995 1.00 92.53 1 A 1 ATOM 6 C CG . MET A 1 1 ? -6.138 3.318 9.268 1.00 89.40 1 A 1 ATOM 7 S SD . MET A 1 1 ? -6.988 1.738 9.075 1.00 87.37 1 A 1 ATOM 8 C CE . MET A 1 1 ? -7.654 1.546 10.720 1.00 78.70 1 A 1 ATOM 9 N N . TRP A 1 2 ? -2.736 5.962 7.062 1.00 93.79 2 A 1 ATOM 10 C CA . TRP A 1 2 ? -1.897 6.348 5.931 1.00 95.38 2 A 1 ATOM 11 C C . TRP A 1 2 ? -0.925 5.237 5.539 1.00 96.81 2 A 1 ATOM 12 O O . TRP A 1 2 ? -0.880 4.813 4.387 1.00 95.70 2 A 1 ATOM 13 C CB . TRP A 1 2 ? -1.120 7.616 6.287 1.00 93.97 2 A 1 ATOM 14 C CG . TRP A 1 2 ? -0.208 8.056 5.193 1.00 91.65 2 A 1 ATOM 15 C CD1 . TRP A 1 2 ? -0.525 8.853 4.141 1.00 90.31 2 A 1 ATOM 16 C CD2 . TRP A 1 2 ? 1.184 7.719 5.028 1.00 91.78 2 A 1 ATOM 17 N NE1 . TRP A 1 2 ? 0.574 9.034 3.333 1.00 88.13 2 A 1 ATOM 18 C CE2 . TRP A 1 2 ? 1.637 8.348 3.849 1.00 90.42 2 A 1 ATOM 19 C CE3 . TRP A 1 2 ? 2.079 6.941 5.771 1.00 88.46 2 A 1 ATOM 20 C CZ2 . TRP A 1 2 ? 2.957 8.220 3.402 1.00 88.87 2 A 1 ATOM 21 C CZ3 . TRP A 1 2 ? 3.394 6.814 5.322 1.00 86.98 2 A 1 ATOM 22 C CH2 . TRP A 1 2 ? 3.821 7.450 4.148 1.00 87.22 2 A 1 ATOM 23 N N . THR A 1 3 ? -0.149 4.750 6.497 1.00 97.77 3 A 1 ATOM 24 C CA . THR A 1 3 ? 0.839 3.700 6.245 1.00 97.99 3 A 1 ATOM 25 C C . THR A 1 3 ? 0.179 2.399 5.796 1.00 98.37 3 A 1 ATOM 26 O O . THR A 1 3 ? 0.659 1.731 4.880 1.00 97.82 3 A 1 ATOM 27 C CB . THR A 1 3 ? 1.676 3.423 7.498 1.00 97.14 3 A 1 ATOM 28 O OG1 . THR A 1 3 ? 2.200 4.644 8.014 1.00 94.50 3 A 1 ATOM 29 C CG2 . THR A 1 3 ? 2.818 2.480 7.176 1.00 93.94 3 A 1 ATOM 30 N N . LEU A 1 4 ? -0.925 2.034 6.430 1.00 97.95 4 A 1 ATOM 31 C CA . LEU A 1 4 ? -1.643 0.799 6.107 1.00 98.22 4 A 1 ATOM 32 C C . LEU A 1 4 ? -2.193 0.841 4.685 1.00 98.45 4 A 1 ATOM 33 O O . LEU A 1 4 ? -2.023 -0.100 3.913 1.00 98.17 4 A 1 ATOM 34 C CB . LEU A 1 4 ? -2.790 0.586 7.100 1.00 97.89 4 A 1 ATOM 35 C CG . LEU A 1 4 ? -2.333 0.304 8.530 1.00 94.97 4 A 1 ATOM 36 C CD1 . LEU A 1 4 ? -3.531 0.248 9.465 1.00 92.89 4 A 1 ATOM 37 C CD2 . LEU A 1 4 ? -1.556 -1.002 8.598 1.00 91.90 4 A 1 ATOM 38 N N . VAL A 1 5 ? -2.864 1.934 4.330 1.00 98.03 5 A 1 ATOM 39 C CA . VAL A 1 5 ? -3.440 2.099 2.995 1.00 98.07 5 A 1 ATOM 40 C C . VAL A 1 5 ? -2.346 2.151 1.934 1.00 98.28 5 A 1 ATOM 41 O O . VAL A 1 5 ? -2.491 1.585 0.846 1.00 97.88 5 A 1 ATOM 42 C CB . VAL A 1 5 ? -4.301 3.370 2.931 1.00 97.46 5 A 1 ATOM 43 C CG1 . VAL A 1 5 ? -4.839 3.589 1.527 1.00 94.94 5 A 1 ATOM 44 C CG2 . VAL A 1 5 ? -5.449 3.281 3.927 1.00 95.22 5 A 1 ATOM 45 N N . SER A 1 6 ? -1.243 2.819 2.252 1.00 98.24 6 A 1 ATOM 46 C CA . SER A 1 6 ? -0.128 2.970 1.322 1.00 98.27 6 A 1 ATOM 47 C C . SER A 1 6 ? 0.523 1.629 1.003 1.00 98.47 6 A 1 ATOM 48 O O . SER A 1 6 ? 0.768 1.312 -0.160 1.00 98.09 6 A 1 ATOM 49 C CB . SER A 1 6 ? 0.917 3.918 1.903 1.00 97.73 6 A 1 ATOM 50 O OG . SER A 1 6 ? 1.990 4.078 1.006 1.00 93.56 6 A 1 ATOM 51 N N . TRP A 1 7 ? 0.806 0.827 2.029 1.00 98.00 7 A 1 ATOM 52 C CA . TRP A 1 7 ? 1.453 -0.466 1.829 1.00 98.10 7 A 1 ATOM 53 C C . TRP A 1 7 ? 0.530 -1.442 1.098 1.00 98.45 7 A 1 ATOM 54 O O . TRP A 1 7 ? 0.975 -2.203 0.238 1.00 98.35 7 A 1 ATOM 55 C CB . TRP A 1 7 ? 1.916 -1.039 3.173 1.00 97.86 7 A 1 ATOM 56 C CG . TRP A 1 7 ? 1.004 -2.066 3.760 1.00 96.94 7 A 1 ATOM 57 C CD1 . TRP A 1 7 ? 0.086 -1.881 4.742 1.00 94.65 7 A 1 ATOM 58 C CD2 . TRP A 1 7 ? 0.914 -3.450 3.380 1.00 95.92 7 A 1 ATOM 59 N NE1 . TRP A 1 7 ? -0.570 -3.057 4.993 1.00 93.73 7 A 1 ATOM 60 C CE2 . TRP A 1 7 ? -0.084 -4.045 4.172 1.00 95.34 7 A 1 ATOM 61 C CE3 . TRP A 1 7 ? 1.586 -4.240 2.442 1.00 94.32 7 A 1 ATOM 62 C CZ2 . TRP A 1 7 ? -0.426 -5.389 4.055 1.00 94.94 7 A 1 ATOM 63 C CZ3 . TRP A 1 7 ? 1.244 -5.582 2.327 1.00 93.36 7 A 1 ATOM 64 C CH2 . TRP A 1 7 ? 0.244 -6.144 3.126 1.00 93.66 7 A 1 ATOM 65 N N . VAL A 1 8 ? -0.759 -1.412 1.411 1.00 98.03 8 A 1 ATOM 66 C CA . VAL A 1 8 ? -1.735 -2.283 0.759 1.00 98.08 8 A 1 ATOM 67 C C . VAL A 1 8 ? -1.826 -1.952 -0.723 1.00 98.31 8 A 1 ATOM 68 O O . VAL A 1 8 ? -1.854 -2.847 -1.573 1.00 98.09 8 A 1 ATOM 69 C CB . VAL A 1 8 ? -3.120 -2.147 1.414 1.00 97.77 8 A 1 ATOM 70 C CG1 . VAL A 1 8 ? -4.169 -2.915 0.620 1.00 96.28 8 A 1 ATOM 71 C CG2 . VAL A 1 8 ? -3.078 -2.662 2.845 1.00 96.34 8 A 1 ATOM 72 N N . ALA A 1 9 ? -1.882 -0.666 -1.044 1.00 97.78 9 A 1 ATOM 73 C CA . ALA A 1 9 ? -1.967 -0.214 -2.428 1.00 97.73 9 A 1 ATOM 74 C C . ALA A 1 9 ? -0.720 -0.609 -3.211 1.00 98.12 9 A 1 ATOM 75 O O . ALA A 1 9 ? -0.807 -0.998 -4.377 1.00 97.63 9 A 1 ATOM 76 C CB . ALA A 1 9 ? -2.153 1.298 -2.465 1.00 97.17 9 A 1 ATOM 77 N N . LEU A 1 10 ? 0.450 -0.521 -2.568 1.00 97.56 10 A 1 ATOM 78 C CA . LEU A 1 10 ? 1.718 -0.871 -3.200 1.00 97.39 10 A 1 ATOM 79 C C . LEU A 1 10 ? 1.755 -2.353 -3.542 1.00 98.05 10 A 1 ATOM 80 O O . LEU A 1 10 ? 2.122 -2.741 -4.656 1.00 97.74 10 A 1 ATOM 81 C CB . LEU A 1 10 ? 2.877 -0.500 -2.269 1.00 96.90 10 A 1 ATOM 82 C CG . LEU A 1 10 ? 4.254 -0.541 -2.935 1.00 93.44 10 A 1 ATOM 83 C CD1 . LEU A 1 10 ? 5.217 0.388 -2.209 1.00 91.14 10 A 1 ATOM 84 C CD2 . LEU A 1 10 ? 4.823 -1.951 -2.954 1.00 90.70 10 A 1 ATOM 85 N N . THR A 1 11 ? 1.372 -3.200 -2.593 1.00 98.14 11 A 1 ATOM 86 C CA . THR A 1 11 ? 1.365 -4.647 -2.800 1.00 98.11 11 A 1 ATOM 87 C C . THR A 1 11 ? 0.368 -5.036 -3.883 1.00 98.38 11 A 1 ATOM 88 O O . THR A 1 11 ? 0.670 -5.856 -4.753 1.00 98.10 11 A 1 ATOM 89 C CB . THR A 1 11 ? 1.008 -5.382 -1.501 1.00 97.47 11 A 1 ATOM 90 O OG1 . THR A 1 11 ? 1.912 -4.995 -0.467 1.00 94.28 11 A 1 ATOM 91 C CG2 . THR A 1 11 ? 1.093 -6.888 -1.694 1.00 94.16 11 A 1 ATOM 92 N N . ALA A 1 12 ? -0.830 -4.446 -3.839 1.00 98.20 12 A 1 ATOM 93 C CA . ALA A 1 12 ? -1.869 -4.733 -4.821 1.00 98.02 12 A 1 ATOM 94 C C . ALA A 1 12 ? -1.425 -4.326 -6.220 1.00 98.28 12 A 1 ATOM 95 O O . ALA A 1 12 ? -1.673 -5.043 -7.192 1.00 97.57 12 A 1 ATOM 96 C CB . ALA A 1 12 ? -3.151 -4.000 -4.445 1.00 97.43 12 A 1 ATOM 97 N N . GLY A 1 13 ? -0.764 -3.184 -6.329 1.00 98.18 13 A 1 ATOM 98 C CA . GLY A 1 13 ? -0.276 -2.698 -7.613 1.00 98.10 13 A 1 ATOM 99 C C . GLY A 1 13 ? 0.793 -3.598 -8.195 1.00 98.38 13 A 1 ATOM 100 O O . GLY A 1 13 ? 0.800 -3.877 -9.395 1.00 97.91 13 A 1 ATOM 101 N N . LEU A 1 14 ? 1.703 -4.080 -7.351 1.00 98.09 14 A 1 ATOM 102 C CA . LEU A 1 14 ? 2.781 -4.966 -7.779 1.00 98.05 14 A 1 ATOM 103 C C . LEU A 1 14 ? 2.222 -6.296 -8.267 1.00 98.32 14 A 1 ATOM 104 O O . LEU A 1 14 ? 2.686 -6.846 -9.270 1.00 97.87 14 A 1 ATOM 105 C CB . LEU A 1 14 ? 3.766 -5.186 -6.623 1.00 97.63 14 A 1 ATOM 106 C CG . LEU A 1 14 ? 5.061 -5.891 -7.034 1.00 95.18 14 A 1 ATOM 107 C CD1 . LEU A 1 14 ? 6.209 -5.441 -6.145 1.00 92.65 14 A 1 ATOM 108 C CD2 . LEU A 1 14 ? 4.923 -7.397 -6.970 1.00 91.71 14 A 1 ATOM 109 N N . VAL A 1 15 ? 1.223 -6.842 -7.561 1.00 98.40 15 A 1 ATOM 110 C CA . VAL A 1 15 ? 0.587 -8.105 -7.940 1.00 98.30 15 A 1 ATOM 111 C C . VAL A 1 15 ? -0.136 -7.968 -9.271 1.00 98.38 15 A 1 ATOM 112 O O . VAL A 1 15 ? -0.053 -8.853 -10.129 1.00 97.90 15 A 1 ATOM 113 C CB . VAL A 1 15 ? -0.403 -8.568 -6.857 1.00 97.55 15 A 1 ATOM 114 C CG1 . VAL A 1 15 ? -1.159 -9.804 -7.320 1.00 95.16 15 A 1 ATOM 115 C CG2 . VAL A 1 15 ? 0.337 -8.866 -5.565 1.00 95.62 15 A 1 ATOM 116 N N . ALA A 1 16 ? -0.854 -6.863 -9.447 1.00 97.48 16 A 1 ATOM 117 C CA . ALA A 1 16 ? -1.600 -6.604 -10.680 1.00 96.92 16 A 1 ATOM 118 C C . ALA A 1 16 ? -0.657 -6.423 -11.864 1.00 97.01 16 A 1 ATOM 119 O O . ALA A 1 16 ? -0.969 -6.839 -12.981 1.00 95.01 16 A 1 ATOM 120 C CB . ALA A 1 16 ? -2.479 -5.370 -10.509 1.00 95.70 16 A 1 ATOM 121 N N . GLY A 1 17 ? 0.506 -5.814 -11.593 1.00 94.95 17 A 1 ATOM 122 C CA . GLY A 1 17 ? 1.504 -5.569 -12.635 1.00 91.77 17 A 1 ATOM 123 C C . GLY A 1 17 ? 1.384 -4.172 -13.211 1.00 89.38 17 A 1 ATOM 124 O O . GLY A 1 17 ? 1.970 -3.917 -14.276 1.00 82.88 17 A 1 ATOM 125 O OXT . GLY A 1 17 ? 0.740 -3.303 -12.593 1.00 88.39 17 A 1 #