# 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_spkb11751 # _entry.id spkb11751 # 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" "C3 H7 N O2 S" 121.158 CYS y CYSTEINE C([C@@H](C(=O)O)N)S ? "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" "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 PRO 3 1 n LEU 4 1 n VAL 5 1 n ALA 6 1 n ALA 7 1 n LEU 8 1 n LEU 9 1 n LEU 10 1 n GLY 11 1 n SER 12 1 n ALA 13 1 n CYS 14 1 n CYS 15 1 n GLY 16 1 n SER 17 1 n ALA 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 @ 2025-07-03 22:29:42)" _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 91.20 _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 89.03 1 1 A TRP 2 2 90.18 1 2 A PRO 3 2 96.59 1 3 A LEU 4 2 95.11 1 4 A VAL 5 2 96.74 1 5 A ALA 6 2 96.68 1 6 A ALA 7 2 95.33 1 7 A LEU 8 2 94.15 1 8 A LEU 9 2 95.02 1 9 A LEU 10 2 93.35 1 10 A GLY 11 2 94.77 1 11 A SER 12 2 92.78 1 12 A ALA 13 2 92.87 1 13 A CYS 14 2 86.14 1 14 A CYS 15 2 83.94 1 15 A GLY 16 2 85.25 1 16 A SER 17 2 82.54 1 17 A ALA 18 2 78.16 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 LEU . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n ALA . 6 A 6 A 7 1 n ALA . 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 SER . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n CYS . 14 A 14 A 15 1 n CYS . 15 A 15 A 16 1 n GLY . 16 A 16 A 17 1 n SER . 17 A 17 A 18 1 n ALA . 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 ? -4.698 3.746 13.784 1.00 94.53 1 A 1 ATOM 2 C CA . MET A 1 1 ? -3.423 3.952 13.061 1.00 94.19 1 A 1 ATOM 3 C C . MET A 1 1 ? -3.682 4.175 11.572 1.00 94.69 1 A 1 ATOM 4 O O . MET A 1 1 ? -3.911 3.228 10.828 1.00 93.19 1 A 1 ATOM 5 C CB . MET A 1 1 ? -2.531 2.731 13.250 1.00 90.94 1 A 1 ATOM 6 C CG . MET A 1 1 ? -1.935 2.688 14.653 1.00 86.51 1 A 1 ATOM 7 S SD . MET A 1 1 ? -0.873 1.259 14.879 1.00 83.65 1 A 1 ATOM 8 C CE . MET A 1 1 ? -0.173 1.641 16.477 1.00 74.53 1 A 1 ATOM 9 N N . TRP A 1 2 ? -3.656 5.425 11.160 1.00 94.37 2 A 1 ATOM 10 C CA . TRP A 1 2 ? -3.894 5.796 9.767 1.00 94.89 2 A 1 ATOM 11 C C . TRP A 1 2 ? -2.661 5.616 8.881 1.00 96.13 2 A 1 ATOM 12 O O . TRP A 1 2 ? -2.783 5.217 7.726 1.00 95.64 2 A 1 ATOM 13 C CB . TRP A 1 2 ? -4.368 7.252 9.715 1.00 93.11 2 A 1 ATOM 14 C CG . TRP A 1 2 ? -5.813 7.375 9.370 1.00 90.60 2 A 1 ATOM 15 C CD1 . TRP A 1 2 ? -6.855 7.450 10.229 1.00 88.46 2 A 1 ATOM 16 C CD2 . TRP A 1 2 ? -6.380 7.447 8.044 1.00 89.83 2 A 1 ATOM 17 N NE1 . TRP A 1 2 ? -8.035 7.562 9.534 1.00 87.78 2 A 1 ATOM 18 C CE2 . TRP A 1 2 ? -7.776 7.561 8.188 1.00 88.51 2 A 1 ATOM 19 C CE3 . TRP A 1 2 ? -5.828 7.428 6.761 1.00 87.23 2 A 1 ATOM 20 C CZ2 . TRP A 1 2 ? -8.625 7.657 7.083 1.00 86.82 2 A 1 ATOM 21 C CZ3 . TRP A 1 2 ? -6.673 7.523 5.665 1.00 84.82 2 A 1 ATOM 22 C CH2 . TRP A 1 2 ? -8.055 7.633 5.832 1.00 84.31 2 A 1 ATOM 23 N N . PRO A 1 3 ? -1.489 5.913 9.413 1.00 97.32 3 A 1 ATOM 24 C CA . PRO A 1 3 ? -0.250 5.791 8.625 1.00 97.40 3 A 1 ATOM 25 C C . PRO A 1 3 ? -0.035 4.385 8.071 1.00 97.72 3 A 1 ATOM 26 O O . PRO A 1 3 ? 0.556 4.217 7.004 1.00 96.67 3 A 1 ATOM 27 C CB . PRO A 1 3 ? 0.853 6.169 9.623 1.00 96.27 3 A 1 ATOM 28 C CG . PRO A 1 3 ? 0.239 5.986 10.971 1.00 94.57 3 A 1 ATOM 29 C CD . PRO A 1 3 ? -1.220 6.313 10.797 1.00 96.18 3 A 1 ATOM 30 N N . LEU A 1 4 ? -0.524 3.379 8.786 1.00 97.13 4 A 1 ATOM 31 C CA . LEU A 1 4 ? -0.377 1.994 8.347 1.00 97.18 4 A 1 ATOM 32 C C . LEU A 1 4 ? -1.216 1.733 7.102 1.00 97.50 4 A 1 ATOM 33 O O . LEU A 1 4 ? -0.751 1.143 6.130 1.00 97.22 4 A 1 ATOM 34 C CB . LEU A 1 4 ? -0.793 1.039 9.476 1.00 96.90 4 A 1 ATOM 35 C CG . LEU A 1 4 ? 0.382 0.487 10.280 1.00 93.50 4 A 1 ATOM 36 C CD1 . LEU A 1 4 ? 1.295 -0.326 9.373 1.00 91.07 4 A 1 ATOM 37 C CD2 . LEU A 1 4 ? 1.154 1.619 10.930 1.00 90.40 4 A 1 ATOM 38 N N . VAL A 1 5 ? -2.464 2.175 7.155 1.00 97.78 5 A 1 ATOM 39 C CA . VAL A 1 5 ? -3.381 1.999 6.026 1.00 97.49 5 A 1 ATOM 40 C C . VAL A 1 5 ? -2.904 2.806 4.821 1.00 97.46 5 A 1 ATOM 41 O O . VAL A 1 5 ? -2.948 2.333 3.682 1.00 97.26 5 A 1 ATOM 42 C CB . VAL A 1 5 ? -4.805 2.435 6.410 1.00 97.03 5 A 1 ATOM 43 C CG1 . VAL A 1 5 ? -5.766 2.181 5.261 1.00 95.04 5 A 1 ATOM 44 C CG2 . VAL A 1 5 ? -5.267 1.697 7.656 1.00 95.14 5 A 1 ATOM 45 N N . ALA A 1 6 ? -2.471 4.016 5.078 1.00 97.26 6 A 1 ATOM 46 C CA . ALA A 1 6 ? -1.993 4.896 4.009 1.00 96.73 6 A 1 ATOM 47 C C . ALA A 1 6 ? -0.757 4.305 3.336 1.00 96.95 6 A 1 ATOM 48 O O . ALA A 1 6 ? -0.627 4.337 2.113 1.00 96.46 6 A 1 ATOM 49 C CB . ALA A 1 6 ? -1.669 6.270 4.581 1.00 96.02 6 A 1 ATOM 50 N N . ALA A 1 7 ? 0.128 3.761 4.133 1.00 95.95 7 A 1 ATOM 51 C CA . ALA A 1 7 ? 1.358 3.164 3.614 1.00 95.27 7 A 1 ATOM 52 C C . ALA A 1 7 ? 1.044 1.941 2.760 1.00 95.91 7 A 1 ATOM 53 O O . ALA A 1 7 ? 1.650 1.731 1.710 1.00 94.92 7 A 1 ATOM 54 C CB . ALA A 1 7 ? 2.270 2.775 4.769 1.00 94.59 7 A 1 ATOM 55 N N . LEU A 1 8 ? 0.089 1.144 3.214 1.00 95.94 8 A 1 ATOM 56 C CA . LEU A 1 8 ? -0.312 -0.058 2.486 1.00 95.62 8 A 1 ATOM 57 C C . LEU A 1 8 ? -0.950 0.308 1.153 1.00 96.24 8 A 1 ATOM 58 O O . LEU A 1 8 ? -0.667 -0.310 0.127 1.00 95.90 8 A 1 ATOM 59 C CB . LEU A 1 8 ? -1.299 -0.865 3.331 1.00 95.51 8 A 1 ATOM 60 C CG . LEU A 1 8 ? -1.530 -2.283 2.822 1.00 92.17 8 A 1 ATOM 61 C CD1 . LEU A 1 8 ? -0.322 -3.156 3.143 1.00 90.91 8 A 1 ATOM 62 C CD2 . LEU A 1 8 ? -2.783 -2.870 3.448 1.00 90.89 8 A 1 ATOM 63 N N . LEU A 1 9 ? -1.814 1.310 1.179 1.00 96.17 9 A 1 ATOM 64 C CA . LEU A 1 9 ? -2.493 1.770 -0.033 1.00 95.86 9 A 1 ATOM 65 C C . LEU A 1 9 ? -1.488 2.288 -1.054 1.00 96.20 9 A 1 ATOM 66 O O . LEU A 1 9 ? -1.525 1.908 -2.225 1.00 96.01 9 A 1 ATOM 67 C CB . LEU A 1 9 ? -3.492 2.878 0.331 1.00 95.81 9 A 1 ATOM 68 C CG . LEU A 1 9 ? -4.937 2.382 0.411 1.00 93.95 9 A 1 ATOM 69 C CD1 . LEU A 1 9 ? -5.756 3.258 1.347 1.00 93.23 9 A 1 ATOM 70 C CD2 . LEU A 1 9 ? -5.555 2.367 -0.976 1.00 92.96 9 A 1 ATOM 71 N N . LEU A 1 10 ? -0.604 3.140 -0.607 1.00 95.68 10 A 1 ATOM 72 C CA . LEU A 1 10 ? 0.411 3.717 -1.489 1.00 94.82 10 A 1 ATOM 73 C C . LEU A 1 10 ? 1.351 2.638 -2.013 1.00 95.35 10 A 1 ATOM 74 O O . LEU A 1 10 ? 1.675 2.603 -3.197 1.00 94.76 10 A 1 ATOM 75 C CB . LEU A 1 10 ? 1.210 4.781 -0.739 1.00 94.14 10 A 1 ATOM 76 C CG . LEU A 1 10 ? 1.306 6.106 -1.487 1.00 91.46 10 A 1 ATOM 77 C CD1 . LEU A 1 10 ? 0.084 6.968 -1.188 1.00 90.56 10 A 1 ATOM 78 C CD2 . LEU A 1 10 ? 2.574 6.835 -1.086 1.00 90.06 10 A 1 ATOM 79 N N . GLY A 1 11 ? 1.757 1.764 -1.132 1.00 95.15 11 A 1 ATOM 80 C CA . GLY A 1 11 ? 2.656 0.680 -1.517 1.00 94.45 11 A 1 ATOM 81 C C . GLY A 1 11 ? 1.994 -0.286 -2.475 1.00 95.17 11 A 1 ATOM 82 O O . GLY A 1 11 ? 2.632 -0.800 -3.389 1.00 94.32 11 A 1 ATOM 83 N N . SER A 1 12 ? 0.704 -0.529 -2.278 1.00 95.18 12 A 1 ATOM 84 C CA . SER A 1 12 ? -0.057 -1.434 -3.137 1.00 94.84 12 A 1 ATOM 85 C C . SER A 1 12 ? -0.073 -0.926 -4.569 1.00 94.82 12 A 1 ATOM 86 O O . SER A 1 12 ? 0.119 -1.695 -5.511 1.00 92.45 12 A 1 ATOM 87 C CB . SER A 1 12 ? -1.491 -1.560 -2.627 1.00 93.59 12 A 1 ATOM 88 O OG . SER A 1 12 ? -2.188 -2.529 -3.363 1.00 85.80 12 A 1 ATOM 89 N N . ALA A 1 13 ? -0.315 0.369 -4.735 1.00 94.45 13 A 1 ATOM 90 C CA . ALA A 1 13 ? -0.351 0.987 -6.059 1.00 93.55 13 A 1 ATOM 91 C C . ALA A 1 13 ? 1.008 0.889 -6.741 1.00 93.48 13 A 1 ATOM 92 O O . ALA A 1 13 ? 1.100 0.592 -7.931 1.00 90.39 13 A 1 ATOM 93 C CB . ALA A 1 13 ? -0.776 2.444 -5.941 1.00 92.49 13 A 1 ATOM 94 N N . CYS A 1 14 ? 2.052 1.132 -5.987 1.00 90.05 14 A 1 ATOM 95 C CA . CYS A 1 14 ? 3.410 1.073 -6.526 1.00 88.82 14 A 1 ATOM 96 C C . CYS A 1 14 ? 4.353 0.478 -5.484 1.00 89.16 14 A 1 ATOM 97 O O . CYS A 1 14 ? 4.842 1.180 -4.608 1.00 84.51 14 A 1 ATOM 98 C CB . CYS A 1 14 ? 3.864 2.484 -6.904 1.00 85.47 14 A 1 ATOM 99 S SG . CYS A 1 14 ? 5.070 2.482 -8.233 1.00 78.86 14 A 1 ATOM 100 N N . CYS A 1 15 ? 4.594 -0.814 -5.617 1.00 87.15 15 A 1 ATOM 101 C CA . CYS A 1 15 ? 5.463 -1.519 -4.666 1.00 86.66 15 A 1 ATOM 102 C C . CYS A 1 15 ? 6.698 -0.687 -4.312 1.00 87.31 15 A 1 ATOM 103 O O . CYS A 1 15 ? 7.210 -0.749 -3.198 1.00 81.42 15 A 1 ATOM 104 C CB . CYS A 1 15 ? 5.900 -2.862 -5.258 1.00 83.29 15 A 1 ATOM 105 S SG . CYS A 1 15 ? 6.159 -4.091 -3.961 1.00 77.83 15 A 1 ATOM 106 N N . GLY A 1 16 ? 7.177 0.051 -5.297 1.00 85.10 16 A 1 ATOM 107 C CA . GLY A 1 16 ? 8.323 0.930 -5.054 1.00 84.56 16 A 1 ATOM 108 C C . GLY A 1 16 ? 8.966 1.359 -6.347 1.00 86.60 16 A 1 ATOM 109 O O . GLY A 1 16 ? 8.504 2.291 -7.001 1.00 84.74 16 A 1 ATOM 110 N N . SER A 1 17 ? 10.019 0.681 -6.733 1.00 85.40 17 A 1 ATOM 111 C CA . SER A 1 17 ? 10.739 1.025 -7.962 1.00 85.72 17 A 1 ATOM 112 C C . SER A 1 17 ? 11.631 -0.138 -8.379 1.00 86.51 17 A 1 ATOM 113 O O . SER A 1 17 ? 11.213 -1.292 -8.360 1.00 81.23 17 A 1 ATOM 114 C CB . SER A 1 17 ? 11.562 2.290 -7.720 1.00 82.74 17 A 1 ATOM 115 O OG . SER A 1 17 ? 12.315 2.171 -6.530 1.00 73.62 17 A 1 ATOM 116 N N . ALA A 1 18 ? 12.863 0.176 -8.776 1.00 84.39 18 A 1 ATOM 117 C CA . ALA A 1 18 ? 13.789 -0.868 -9.206 1.00 82.52 18 A 1 ATOM 118 C C . ALA A 1 18 ? 14.196 -1.754 -8.035 1.00 81.44 18 A 1 ATOM 119 O O . ALA A 1 18 ? 14.208 -1.272 -6.897 1.00 74.52 18 A 1 ATOM 120 C CB . ALA A 1 18 ? 15.026 -0.233 -9.838 1.00 75.43 18 A 1 ATOM 121 O OXT . ALA A 1 18 ? 14.507 -2.945 -8.275 1.00 70.63 18 A 1 #