# 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_spkb21941 # _entry.id spkb21941 # 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" "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 PRO 2 1 n THR 3 1 n TRP 4 1 n LEU 5 1 n TRP 6 1 n GLY 7 1 n LEU 8 1 n LEU 9 1 n LEU 10 1 n THR 11 1 n ALA 12 1 n GLY 13 1 n THR 14 1 n LEU 15 1 n SER 16 1 n ALA 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 01:25:50)" _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 92.53 _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 80.54 1 1 A PRO 2 2 92.82 1 2 A THR 3 2 95.36 1 3 A TRP 4 2 93.04 1 4 A LEU 5 2 94.11 1 5 A TRP 6 2 92.40 1 6 A GLY 7 2 96.75 1 7 A LEU 8 2 94.59 1 8 A LEU 9 2 94.76 1 9 A LEU 10 2 95.12 1 10 A THR 11 2 94.89 1 11 A ALA 12 2 95.83 1 12 A GLY 13 2 95.82 1 13 A THR 14 2 92.16 1 14 A LEU 15 2 91.75 1 15 A SER 16 2 91.86 1 16 A ALA 17 2 84.32 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 PRO . 2 A 2 A 3 1 n THR . 3 A 3 A 4 1 n TRP . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n TRP . 6 A 6 A 7 1 n GLY . 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 THR . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n GLY . 13 A 13 A 14 1 n THR . 14 A 14 A 15 1 n LEU . 15 A 15 A 16 1 n SER . 16 A 16 A 17 1 n ALA . 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 ? 0.609 -8.965 7.852 1.00 85.07 1 A 1 ATOM 2 C CA . MET A 1 1 ? 0.799 -7.846 6.912 1.00 86.95 1 A 1 ATOM 3 C C . MET A 1 1 ? -0.205 -7.929 5.768 1.00 88.68 1 A 1 ATOM 4 O O . MET A 1 1 ? 0.037 -8.613 4.773 1.00 87.70 1 A 1 ATOM 5 C CB . MET A 1 1 ? 2.214 -7.869 6.337 1.00 80.36 1 A 1 ATOM 6 C CG . MET A 1 1 ? 3.273 -7.636 7.396 1.00 75.95 1 A 1 ATOM 7 S SD . MET A 1 1 ? 4.936 -7.679 6.707 1.00 73.18 1 A 1 ATOM 8 C CE . MET A 1 1 ? 5.887 -7.260 8.157 1.00 66.43 1 A 1 ATOM 9 N N . PRO A 1 2 ? -1.330 -7.254 5.893 1.00 92.63 2 A 1 ATOM 10 C CA . PRO A 1 2 ? -2.373 -7.252 4.868 1.00 94.84 2 A 1 ATOM 11 C C . PRO A 1 2 ? -1.967 -6.442 3.636 1.00 96.11 2 A 1 ATOM 12 O O . PRO A 1 2 ? -1.176 -5.500 3.735 1.00 94.25 2 A 1 ATOM 13 C CB . PRO A 1 2 ? -3.564 -6.608 5.579 1.00 91.74 2 A 1 ATOM 14 C CG . PRO A 1 2 ? -2.956 -5.755 6.633 1.00 88.83 2 A 1 ATOM 15 C CD . PRO A 1 2 ? -1.693 -6.458 7.060 1.00 91.35 2 A 1 ATOM 16 N N . THR A 1 3 ? -2.528 -6.816 2.474 1.00 96.68 3 A 1 ATOM 17 C CA . THR A 1 3 ? -2.220 -6.136 1.216 1.00 97.04 3 A 1 ATOM 18 C C . THR A 1 3 ? -2.767 -4.713 1.193 1.00 97.44 3 A 1 ATOM 19 O O . THR A 1 3 ? -2.145 -3.808 0.634 1.00 96.80 3 A 1 ATOM 20 C CB . THR A 1 3 ? -2.807 -6.915 0.037 1.00 95.91 3 A 1 ATOM 21 O OG1 . THR A 1 3 ? -2.435 -8.288 0.132 1.00 92.41 3 A 1 ATOM 22 C CG2 . THR A 1 3 ? -2.311 -6.352 -1.278 1.00 91.21 3 A 1 ATOM 23 N N . TRP A 1 4 ? -3.929 -4.530 1.803 1.00 95.66 4 A 1 ATOM 24 C CA . TRP A 1 4 ? -4.567 -3.213 1.835 1.00 95.62 4 A 1 ATOM 25 C C . TRP A 1 4 ? -3.688 -2.188 2.546 1.00 96.36 4 A 1 ATOM 26 O O . TRP A 1 4 ? -3.767 -0.993 2.263 1.00 95.83 4 A 1 ATOM 27 C CB . TRP A 1 4 ? -5.923 -3.311 2.528 1.00 94.80 4 A 1 ATOM 28 C CG . TRP A 1 4 ? -5.838 -3.773 3.948 1.00 93.82 4 A 1 ATOM 29 C CD1 . TRP A 1 4 ? -5.837 -5.056 4.387 1.00 92.40 4 A 1 ATOM 30 C CD2 . TRP A 1 4 ? -5.732 -2.946 5.119 1.00 93.34 4 A 1 ATOM 31 N NE1 . TRP A 1 4 ? -5.734 -5.084 5.756 1.00 91.03 4 A 1 ATOM 32 C CE2 . TRP A 1 4 ? -5.670 -3.799 6.233 1.00 92.24 4 A 1 ATOM 33 C CE3 . TRP A 1 4 ? -5.691 -1.567 5.325 1.00 91.64 4 A 1 ATOM 34 C CZ2 . TRP A 1 4 ? -5.562 -3.312 7.536 1.00 91.48 4 A 1 ATOM 35 C CZ3 . TRP A 1 4 ? -5.582 -1.085 6.625 1.00 89.34 4 A 1 ATOM 36 C CH2 . TRP A 1 4 ? -5.516 -1.953 7.710 1.00 88.94 4 A 1 ATOM 37 N N . LEU A 1 5 ? -2.848 -2.651 3.442 1.00 96.28 5 A 1 ATOM 38 C CA . LEU A 1 5 ? -1.943 -1.778 4.185 1.00 96.24 5 A 1 ATOM 39 C C . LEU A 1 5 ? -0.940 -1.119 3.244 1.00 96.58 5 A 1 ATOM 40 O O . LEU A 1 5 ? -0.548 0.031 3.437 1.00 96.63 5 A 1 ATOM 41 C CB . LEU A 1 5 ? -1.203 -2.581 5.256 1.00 95.86 5 A 1 ATOM 42 C CG . LEU A 1 5 ? -0.376 -1.729 6.209 1.00 92.06 5 A 1 ATOM 43 C CD1 . LEU A 1 5 ? -1.274 -0.803 7.019 1.00 89.99 5 A 1 ATOM 44 C CD2 . LEU A 1 5 ? 0.429 -2.619 7.141 1.00 89.22 5 A 1 ATOM 45 N N . TRP A 1 6 ? -0.523 -1.860 2.209 1.00 95.59 6 A 1 ATOM 46 C CA . TRP A 1 6 ? 0.420 -1.337 1.222 1.00 95.38 6 A 1 ATOM 47 C C . TRP A 1 6 ? -0.185 -0.174 0.450 1.00 95.91 6 A 1 ATOM 48 O O . TRP A 1 6 ? 0.528 0.745 0.042 1.00 95.94 6 A 1 ATOM 49 C CB . TRP A 1 6 ? 0.830 -2.454 0.260 1.00 94.93 6 A 1 ATOM 50 C CG . TRP A 1 6 ? 1.725 -3.463 0.904 1.00 93.76 6 A 1 ATOM 51 C CD1 . TRP A 1 6 ? 1.447 -4.765 1.156 1.00 90.51 6 A 1 ATOM 52 C CD2 . TRP A 1 6 ? 3.061 -3.234 1.374 1.00 92.23 6 A 1 ATOM 53 N NE1 . TRP A 1 6 ? 2.525 -5.361 1.758 1.00 89.80 6 A 1 ATOM 54 C CE2 . TRP A 1 6 ? 3.535 -4.445 1.908 1.00 91.39 6 A 1 ATOM 55 C CE3 . TRP A 1 6 ? 3.905 -2.120 1.392 1.00 90.86 6 A 1 ATOM 56 C CZ2 . TRP A 1 6 ? 4.812 -4.563 2.455 1.00 90.43 6 A 1 ATOM 57 C CZ3 . TRP A 1 6 ? 5.170 -2.244 1.936 1.00 88.34 6 A 1 ATOM 58 C CH2 . TRP A 1 6 ? 5.614 -3.456 2.463 1.00 88.60 6 A 1 ATOM 59 N N . GLY A 1 7 ? -1.497 -0.215 0.259 1.00 96.60 7 A 1 ATOM 60 C CA . GLY A 1 7 ? -2.190 0.867 -0.433 1.00 96.53 7 A 1 ATOM 61 C C . GLY A 1 7 ? -2.062 2.179 0.314 1.00 97.08 7 A 1 ATOM 62 O O . GLY A 1 7 ? -1.823 3.229 -0.287 1.00 96.79 7 A 1 ATOM 63 N N . LEU A 1 8 ? -2.201 2.111 1.619 1.00 96.35 8 A 1 ATOM 64 C CA . LEU A 1 8 ? -2.071 3.293 2.465 1.00 95.96 8 A 1 ATOM 65 C C . LEU A 1 8 ? -0.635 3.806 2.452 1.00 96.44 8 A 1 ATOM 66 O O . LEU A 1 8 ? -0.393 5.013 2.396 1.00 96.06 8 A 1 ATOM 67 C CB . LEU A 1 8 ? -2.493 2.953 3.892 1.00 95.60 8 A 1 ATOM 68 C CG . LEU A 1 8 ? -2.412 4.123 4.866 1.00 93.37 8 A 1 ATOM 69 C CD1 . LEU A 1 8 ? -3.383 5.222 4.468 1.00 91.72 8 A 1 ATOM 70 C CD2 . LEU A 1 8 ? -2.699 3.644 6.279 1.00 91.23 8 A 1 ATOM 71 N N . LEU A 1 9 ? 0.306 2.873 2.496 1.00 96.24 9 A 1 ATOM 72 C CA . LEU A 1 9 ? 1.726 3.213 2.485 1.00 96.05 9 A 1 ATOM 73 C C . LEU A 1 9 ? 2.110 3.873 1.168 1.00 96.48 9 A 1 ATOM 74 O O . LEU A 1 9 ? 2.888 4.829 1.138 1.00 96.40 9 A 1 ATOM 75 C CB . LEU A 1 9 ? 2.557 1.947 2.721 1.00 95.72 9 A 1 ATOM 76 C CG . LEU A 1 9 ? 3.945 2.198 3.314 1.00 93.48 9 A 1 ATOM 77 C CD1 . LEU A 1 9 ? 4.546 0.892 3.813 1.00 92.12 9 A 1 ATOM 78 C CD2 . LEU A 1 9 ? 4.874 2.836 2.300 1.00 91.60 9 A 1 ATOM 79 N N . LEU A 1 10 ? 1.556 3.358 0.073 1.00 96.41 10 A 1 ATOM 80 C CA . LEU A 1 10 ? 1.831 3.902 -1.257 1.00 96.27 10 A 1 ATOM 81 C C . LEU A 1 10 ? 1.349 5.343 -1.365 1.00 96.74 10 A 1 ATOM 82 O O . LEU A 1 10 ? 2.048 6.204 -1.905 1.00 96.45 10 A 1 ATOM 83 C CB . LEU A 1 10 ? 1.149 3.042 -2.320 1.00 96.01 10 A 1 ATOM 84 C CG . LEU A 1 10 ? 1.357 3.521 -3.752 1.00 94.21 10 A 1 ATOM 85 C CD1 . LEU A 1 10 ? 2.828 3.465 -4.136 1.00 92.77 10 A 1 ATOM 86 C CD2 . LEU A 1 10 ? 0.533 2.677 -4.710 1.00 92.14 10 A 1 ATOM 87 N N . THR A 1 11 ? 0.162 5.594 -0.855 1.00 96.60 11 A 1 ATOM 88 C CA . THR A 1 11 ? -0.415 6.936 -0.896 1.00 96.33 11 A 1 ATOM 89 C C . THR A 1 11 ? 0.435 7.917 -0.096 1.00 96.70 11 A 1 ATOM 90 O O . THR A 1 11 ? 0.709 9.032 -0.549 1.00 96.02 11 A 1 ATOM 91 C CB . THR A 1 11 ? -1.840 6.929 -0.332 1.00 95.22 11 A 1 ATOM 92 O OG1 . THR A 1 11 ? -2.625 5.958 -1.022 1.00 91.71 11 A 1 ATOM 93 C CG2 . THR A 1 11 ? -2.487 8.291 -0.491 1.00 91.66 11 A 1 ATOM 94 N N . ALA A 1 12 ? 0.859 7.489 1.085 1.00 96.34 12 A 1 ATOM 95 C CA . ALA A 1 12 ? 1.693 8.330 1.936 1.00 96.02 12 A 1 ATOM 96 C C . ALA A 1 12 ? 3.083 8.506 1.335 1.00 96.53 12 A 1 ATOM 97 O O . ALA A 1 12 ? 3.701 9.565 1.473 1.00 95.40 12 A 1 ATOM 98 C CB . ALA A 1 12 ? 1.793 7.713 3.325 1.00 94.86 12 A 1 ATOM 99 N N . GLY A 1 13 ? 3.568 7.462 0.667 1.00 95.81 13 A 1 ATOM 100 C CA . GLY A 1 13 ? 4.880 7.506 0.038 1.00 95.42 13 A 1 ATOM 101 C C . GLY A 1 13 ? 4.938 8.478 -1.116 1.00 96.41 13 A 1 ATOM 102 O O . GLY A 1 13 ? 5.854 9.293 -1.210 1.00 95.66 13 A 1 ATOM 103 N N . THR A 1 14 ? 3.954 8.402 -2.013 1.00 94.73 14 A 1 ATOM 104 C CA . THR A 1 14 ? 3.908 9.283 -3.178 1.00 94.73 14 A 1 ATOM 105 C C . THR A 1 14 ? 3.684 10.733 -2.763 1.00 95.18 14 A 1 ATOM 106 O O . THR A 1 14 ? 4.167 11.654 -3.424 1.00 93.73 14 A 1 ATOM 107 C CB . THR A 1 14 ? 2.806 8.844 -4.153 1.00 92.91 14 A 1 ATOM 108 O OG1 . THR A 1 14 ? 2.838 9.678 -5.307 1.00 87.27 14 A 1 ATOM 109 C CG2 . THR A 1 14 ? 1.435 8.945 -3.522 1.00 86.57 14 A 1 ATOM 110 N N . LEU A 1 15 ? 2.970 10.927 -1.672 1.00 95.67 15 A 1 ATOM 111 C CA . LEU A 1 15 ? 2.698 12.263 -1.159 1.00 94.93 15 A 1 ATOM 112 C C . LEU A 1 15 ? 3.939 12.843 -0.487 1.00 95.34 15 A 1 ATOM 113 O O . LEU A 1 15 ? 4.238 14.034 -0.620 1.00 94.05 15 A 1 ATOM 114 C CB . LEU A 1 15 ? 1.526 12.215 -0.168 1.00 93.43 15 A 1 ATOM 115 C CG . LEU A 1 15 ? 0.780 13.535 0.037 1.00 90.02 15 A 1 ATOM 116 C CD1 . LEU A 1 15 ? 1.674 14.593 0.651 1.00 86.86 15 A 1 ATOM 117 C CD2 . LEU A 1 15 ? 0.216 14.020 -1.292 1.00 83.72 15 A 1 ATOM 118 N N . SER A 1 16 ? 4.649 11.999 0.234 1.00 94.93 16 A 1 ATOM 119 C CA . SER A 1 16 ? 5.858 12.422 0.937 1.00 94.62 16 A 1 ATOM 120 C C . SER A 1 16 ? 7.058 12.513 0.003 1.00 94.58 16 A 1 ATOM 121 O O . SER A 1 16 ? 7.981 13.295 0.244 1.00 91.83 16 A 1 ATOM 122 C CB . SER A 1 16 ? 6.169 11.452 2.074 1.00 92.28 16 A 1 ATOM 123 O OG . SER A 1 16 ? 5.117 11.438 3.020 1.00 82.90 16 A 1 ATOM 124 N N . ALA A 1 17 ? 7.034 11.702 -1.053 1.00 90.74 17 A 1 ATOM 125 C CA . ALA A 1 17 ? 8.133 11.663 -2.018 1.00 88.34 17 A 1 ATOM 126 C C . ALA A 1 17 ? 7.931 12.706 -3.114 1.00 86.71 17 A 1 ATOM 127 O O . ALA A 1 17 ? 8.868 12.972 -3.878 1.00 82.34 17 A 1 ATOM 128 C CB . ALA A 1 17 ? 8.248 10.261 -2.618 1.00 82.83 17 A 1 ATOM 129 O OXT . ALA A 1 17 ? 6.833 13.270 -3.220 1.00 74.96 17 A 1 #