# 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_spkb15941 # _entry.id spkb15941 # 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" "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" "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 TRP 2 1 n PRO 3 1 n GLY 4 1 n PRO 5 1 n ALA 6 1 n LEU 7 1 n LEU 8 1 n LEU 9 1 n LEU 10 1 n GLY 11 1 n LEU 12 1 n GLY 13 1 n LEU 14 1 n GLY 15 1 n LEU 16 1 n GLY 17 1 n SER 18 # _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 @ 2025-07-08 19:38:49)" _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 84.28 _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 77.16 1 1 A TRP 2 2 77.92 1 2 A PRO 3 2 86.07 1 3 A GLY 4 2 90.55 1 4 A PRO 5 2 90.29 1 5 A ALA 6 2 90.17 1 6 A LEU 7 2 86.17 1 7 A LEU 8 2 86.55 1 8 A LEU 9 2 87.63 1 9 A LEU 10 2 86.84 1 10 A GLY 11 2 89.29 1 11 A LEU 12 2 87.05 1 12 A GLY 13 2 89.44 1 13 A LEU 14 2 84.98 1 14 A GLY 15 2 88.27 1 15 A LEU 16 2 82.67 1 16 A GLY 17 2 78.78 1 17 A SER 18 2 70.92 1 18 # _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 PRO . 3 A 3 A 4 1 n GLY . 4 A 4 A 5 1 n PRO . 5 A 5 A 6 1 n ALA . 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 GLY . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n GLY . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n GLY . 15 A 15 A 16 1 n LEU . 16 A 16 A 17 1 n GLY . 17 A 17 A 18 1 n SER . 18 A 18 # _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 ? -6.793 4.364 14.751 1.00 81.01 1 A 1 ATOM 2 C CA . MET A 1 1 ? -6.668 2.919 14.491 1.00 83.55 1 A 1 ATOM 3 C C . MET A 1 1 ? -7.671 2.495 13.416 1.00 85.51 1 A 1 ATOM 4 O O . MET A 1 1 ? -8.648 1.806 13.686 1.00 82.46 1 A 1 ATOM 5 C CB . MET A 1 1 ? -6.939 2.148 15.784 1.00 78.31 1 A 1 ATOM 6 C CG . MET A 1 1 ? -5.894 2.464 16.846 1.00 73.33 1 A 1 ATOM 7 S SD . MET A 1 1 ? -6.450 2.037 18.502 1.00 70.15 1 A 1 ATOM 8 C CE . MET A 1 1 ? -5.133 2.736 19.476 1.00 62.93 1 A 1 ATOM 9 N N . TRP A 1 2 ? -7.408 2.958 12.190 1.00 81.32 2 A 1 ATOM 10 C CA . TRP A 1 2 ? -8.291 2.640 11.079 1.00 85.22 2 A 1 ATOM 11 C C . TRP A 1 2 ? -7.452 2.188 9.874 1.00 88.16 2 A 1 ATOM 12 O O . TRP A 1 2 ? -6.253 2.473 9.808 1.00 86.57 2 A 1 ATOM 13 C CB . TRP A 1 2 ? -9.132 3.881 10.750 1.00 81.11 2 A 1 ATOM 14 C CG . TRP A 1 2 ? -8.630 4.700 9.590 1.00 77.17 2 A 1 ATOM 15 C CD1 . TRP A 1 2 ? -9.327 4.971 8.454 1.00 76.26 2 A 1 ATOM 16 C CD2 . TRP A 1 2 ? -7.364 5.369 9.444 1.00 78.05 2 A 1 ATOM 17 N NE1 . TRP A 1 2 ? -8.586 5.772 7.618 1.00 73.82 2 A 1 ATOM 18 C CE2 . TRP A 1 2 ? -7.372 6.028 8.198 1.00 76.02 2 A 1 ATOM 19 C CE3 . TRP A 1 2 ? -6.233 5.469 10.250 1.00 72.71 2 A 1 ATOM 20 C CZ2 . TRP A 1 2 ? -6.278 6.787 7.741 1.00 73.00 2 A 1 ATOM 21 C CZ3 . TRP A 1 2 ? -5.137 6.223 9.801 1.00 70.94 2 A 1 ATOM 22 C CH2 . TRP A 1 2 ? -5.174 6.869 8.562 1.00 70.47 2 A 1 ATOM 23 N N . PRO A 1 3 ? -8.062 1.463 8.907 1.00 87.79 3 A 1 ATOM 24 C CA . PRO A 1 3 ? -7.346 0.958 7.727 1.00 88.69 3 A 1 ATOM 25 C C . PRO A 1 3 ? -6.901 2.074 6.780 1.00 89.84 3 A 1 ATOM 26 O O . PRO A 1 3 ? -7.382 2.184 5.652 1.00 84.89 3 A 1 ATOM 27 C CB . PRO A 1 3 ? -8.377 0.029 7.069 1.00 84.78 3 A 1 ATOM 28 C CG . PRO A 1 3 ? -9.706 0.570 7.498 1.00 81.27 3 A 1 ATOM 29 C CD . PRO A 1 3 ? -9.476 1.070 8.914 1.00 85.21 3 A 1 ATOM 30 N N . GLY A 1 4 ? -5.973 2.913 7.248 1.00 90.96 4 A 1 ATOM 31 C CA . GLY A 1 4 ? -5.458 4.016 6.440 1.00 90.30 4 A 1 ATOM 32 C C . GLY A 1 4 ? -4.058 3.718 5.933 1.00 91.15 4 A 1 ATOM 33 O O . GLY A 1 4 ? -3.844 3.505 4.740 1.00 89.78 4 A 1 ATOM 34 N N . PRO A 1 5 ? -3.078 3.687 6.842 1.00 91.53 5 A 1 ATOM 35 C CA . PRO A 1 5 ? -1.693 3.379 6.464 1.00 91.83 5 A 1 ATOM 36 C C . PRO A 1 5 ? -1.563 1.990 5.846 1.00 92.34 5 A 1 ATOM 37 O O . PRO A 1 5 ? -0.678 1.746 5.026 1.00 89.77 5 A 1 ATOM 38 C CB . PRO A 1 5 ? -0.925 3.483 7.793 1.00 89.01 5 A 1 ATOM 39 C CG . PRO A 1 5 ? -1.977 3.355 8.854 1.00 87.23 5 A 1 ATOM 40 C CD . PRO A 1 5 ? -3.210 3.986 8.271 1.00 90.34 5 A 1 ATOM 41 N N . ALA A 1 6 ? -2.450 1.083 6.235 1.00 90.95 6 A 1 ATOM 42 C CA . ALA A 1 6 ? -2.432 -0.277 5.685 1.00 90.84 6 A 1 ATOM 43 C C . ALA A 1 6 ? -2.609 -0.223 4.165 1.00 91.15 6 A 1 ATOM 44 O O . ALA A 1 6 ? -1.927 -0.927 3.423 1.00 88.50 6 A 1 ATOM 45 C CB . ALA A 1 6 ? -3.554 -1.091 6.323 1.00 89.40 6 A 1 ATOM 46 N N . LEU A 1 7 ? -3.539 0.641 3.713 1.00 89.81 7 A 1 ATOM 47 C CA . LEU A 1 7 ? -3.784 0.801 2.277 1.00 88.99 7 A 1 ATOM 48 C C . LEU A 1 7 ? -2.540 1.375 1.603 1.00 89.63 7 A 1 ATOM 49 O O . LEU A 1 7 ? -2.168 0.969 0.506 1.00 88.10 7 A 1 ATOM 50 C CB . LEU A 1 7 ? -4.984 1.738 2.054 1.00 87.90 7 A 1 ATOM 51 C CG . LEU A 1 7 ? -6.296 0.990 1.806 1.00 83.68 7 A 1 ATOM 52 C CD1 . LEU A 1 7 ? -6.194 0.155 0.548 1.00 81.30 7 A 1 ATOM 53 C CD2 . LEU A 1 7 ? -6.630 0.114 3.001 1.00 79.95 7 A 1 ATOM 54 N N . LEU A 1 8 ? -1.903 2.332 2.280 1.00 89.10 8 A 1 ATOM 55 C CA . LEU A 1 8 ? -0.687 2.961 1.758 1.00 88.72 8 A 1 ATOM 56 C C . LEU A 1 8 ? 0.397 1.896 1.591 1.00 89.76 8 A 1 ATOM 57 O O . LEU A 1 8 ? 1.086 1.845 0.570 1.00 88.65 8 A 1 ATOM 58 C CB . LEU A 1 8 ? -0.226 4.054 2.737 1.00 88.26 8 A 1 ATOM 59 C CG . LEU A 1 8 ? 0.867 4.965 2.177 1.00 84.87 8 A 1 ATOM 60 C CD1 . LEU A 1 8 ? 2.196 4.228 2.112 1.00 82.04 8 A 1 ATOM 61 C CD2 . LEU A 1 8 ? 0.469 5.467 0.790 1.00 81.02 8 A 1 ATOM 62 N N . LEU A 1 9 ? 0.544 1.048 2.600 1.00 89.20 9 A 1 ATOM 63 C CA . LEU A 1 9 ? 1.539 -0.030 2.550 1.00 89.34 9 A 1 ATOM 64 C C . LEU A 1 9 ? 1.201 -0.994 1.411 1.00 89.94 9 A 1 ATOM 65 O O . LEU A 1 9 ? 2.089 -1.532 0.750 1.00 88.83 9 A 1 ATOM 66 C CB . LEU A 1 9 ? 1.557 -0.785 3.891 1.00 88.63 9 A 1 ATOM 67 C CG . LEU A 1 9 ? 2.597 -0.240 4.880 1.00 86.75 9 A 1 ATOM 68 C CD1 . LEU A 1 9 ? 3.989 -0.397 4.299 1.00 84.51 9 A 1 ATOM 69 C CD2 . LEU A 1 9 ? 2.316 1.221 5.194 1.00 83.88 9 A 1 ATOM 70 N N . LEU A 1 10 ? -0.098 -1.203 1.195 1.00 89.41 10 A 1 ATOM 71 C CA . LEU A 1 10 ? -0.560 -2.099 0.129 1.00 89.16 10 A 1 ATOM 72 C C . LEU A 1 10 ? -0.071 -1.585 -1.227 1.00 90.10 10 A 1 ATOM 73 O O . LEU A 1 10 ? 0.489 -2.329 -2.029 1.00 87.67 10 A 1 ATOM 74 C CB . LEU A 1 10 ? -2.102 -2.141 0.143 1.00 87.97 10 A 1 ATOM 75 C CG . LEU A 1 10 ? -2.677 -3.499 -0.283 1.00 85.64 10 A 1 ATOM 76 C CD1 . LEU A 1 10 ? -2.121 -3.922 -1.636 1.00 83.21 10 A 1 ATOM 77 C CD2 . LEU A 1 10 ? -2.341 -4.538 0.776 1.00 81.54 10 A 1 ATOM 78 N N . GLY A 1 11 ? -0.294 -0.285 -1.465 1.00 89.40 11 A 1 ATOM 79 C CA . GLY A 1 11 ? 0.134 0.313 -2.732 1.00 88.96 11 A 1 ATOM 80 C C . GLY A 1 11 ? 1.645 0.301 -2.865 1.00 90.25 11 A 1 ATOM 81 O O . GLY A 1 11 ? 2.185 0.030 -3.940 1.00 88.55 11 A 1 ATOM 82 N N . LEU A 1 12 ? 2.336 0.601 -1.766 1.00 90.30 12 A 1 ATOM 83 C CA . LEU A 1 12 ? 3.802 0.620 -1.760 1.00 89.97 12 A 1 ATOM 84 C C . LEU A 1 12 ? 4.334 -0.778 -2.091 1.00 90.82 12 A 1 ATOM 85 O O . LEU A 1 12 ? 5.265 -0.931 -2.884 1.00 87.71 12 A 1 ATOM 86 C CB . LEU A 1 12 ? 4.289 1.082 -0.370 1.00 88.28 12 A 1 ATOM 87 C CG . LEU A 1 12 ? 5.783 1.411 -0.310 1.00 85.80 12 A 1 ATOM 88 C CD1 . LEU A 1 12 ? 6.610 0.141 -0.316 1.00 82.62 12 A 1 ATOM 89 C CD2 . LEU A 1 12 ? 6.168 2.305 -1.482 1.00 80.89 12 A 1 ATOM 90 N N . GLY A 1 13 ? 3.737 -1.793 -1.477 1.00 90.13 13 A 1 ATOM 91 C CA . GLY A 1 13 ? 4.170 -3.168 -1.734 1.00 89.38 13 A 1 ATOM 92 C C . GLY A 1 13 ? 3.899 -3.574 -3.174 1.00 90.32 13 A 1 ATOM 93 O O . GLY A 1 13 ? 4.659 -4.340 -3.765 1.00 87.95 13 A 1 ATOM 94 N N . LEU A 1 14 ? 2.810 -3.056 -3.738 1.00 89.33 14 A 1 ATOM 95 C CA . LEU A 1 14 ? 2.444 -3.365 -5.123 1.00 88.52 14 A 1 ATOM 96 C C . LEU A 1 14 ? 3.519 -2.845 -6.076 1.00 88.99 14 A 1 ATOM 97 O O . LEU A 1 14 ? 3.935 -3.537 -7.007 1.00 85.75 14 A 1 ATOM 98 C CB . LEU A 1 14 ? 1.086 -2.708 -5.445 1.00 86.26 14 A 1 ATOM 99 C CG . LEU A 1 14 ? 0.386 -3.290 -6.677 1.00 83.68 14 A 1 ATOM 100 C CD1 . LEU A 1 14 ? 1.195 -3.009 -7.935 1.00 80.19 14 A 1 ATOM 101 C CD2 . LEU A 1 14 ? 0.195 -4.793 -6.503 1.00 77.09 14 A 1 ATOM 102 N N . GLY A 1 15 ? 3.967 -1.610 -5.841 1.00 88.77 15 A 1 ATOM 103 C CA . GLY A 1 15 ? 5.002 -1.016 -6.693 1.00 88.03 15 A 1 ATOM 104 C C . GLY A 1 15 ? 6.383 -1.568 -6.389 1.00 89.21 15 A 1 ATOM 105 O O . GLY A 1 15 ? 7.134 -1.919 -7.295 1.00 87.08 15 A 1 ATOM 106 N N . LEU A 1 16 ? 6.732 -1.626 -5.101 1.00 88.44 16 A 1 ATOM 107 C CA . LEU A 1 16 ? 8.040 -2.135 -4.676 1.00 87.31 16 A 1 ATOM 108 C C . LEU A 1 16 ? 8.131 -3.643 -4.913 1.00 87.56 16 A 1 ATOM 109 O O . LEU A 1 16 ? 9.089 -4.133 -5.515 1.00 83.24 16 A 1 ATOM 110 C CB . LEU A 1 16 ? 8.248 -1.800 -3.186 1.00 84.40 16 A 1 ATOM 111 C CG . LEU A 1 16 ? 9.633 -2.159 -2.640 1.00 80.28 16 A 1 ATOM 112 C CD1 . LEU A 1 16 ? 9.756 -3.658 -2.416 1.00 77.09 16 A 1 ATOM 113 C CD2 . LEU A 1 16 ? 10.711 -1.683 -3.615 1.00 73.05 16 A 1 ATOM 114 N N . GLY A 1 17 ? 7.137 -4.381 -4.433 1.00 82.70 17 A 1 ATOM 115 C CA . GLY A 1 17 ? 7.124 -5.838 -4.602 1.00 79.24 17 A 1 ATOM 116 C C . GLY A 1 17 ? 6.417 -6.239 -5.883 1.00 78.68 17 A 1 ATOM 117 O O . GLY A 1 17 ? 5.330 -6.794 -5.848 1.00 74.51 17 A 1 ATOM 118 N N . SER A 1 18 ? 7.043 -5.948 -7.025 1.00 80.16 18 A 1 ATOM 119 C CA . SER A 1 18 ? 6.462 -6.290 -8.326 1.00 76.67 18 A 1 ATOM 120 C C . SER A 1 18 ? 6.413 -7.803 -8.546 1.00 72.79 18 A 1 ATOM 121 O O . SER A 1 18 ? 6.932 -8.557 -7.703 1.00 65.91 18 A 1 ATOM 122 C CB . SER A 1 18 ? 7.277 -5.648 -9.455 1.00 69.78 18 A 1 ATOM 123 O OG . SER A 1 18 ? 6.679 -5.920 -10.719 1.00 64.25 18 A 1 ATOM 124 O OXT . SER A 1 18 ? 5.869 -8.263 -9.551 1.00 66.85 18 A 1 #