# 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_spkb19382 # _entry.id spkb19382 # 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 ILE y ISOLEUCINE CC[C@H](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" "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 LEU 2 1 n LEU 3 1 n ALA 4 1 n ILE 5 1 n GLY 6 1 n VAL 7 1 n ILE 8 1 n VAL 9 1 n TRP 10 1 n CYS 11 1 n TRP 12 1 n GLY 13 1 n LEU 14 1 n LEU 15 1 n SER 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 @ 2025-07-06 11:27:43)" _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 96.36 _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 92.26 1 1 A LEU 2 2 95.21 1 2 A LEU 3 2 96.15 1 3 A ALA 4 2 98.30 1 4 A ILE 5 2 97.28 1 5 A GLY 6 2 98.39 1 6 A VAL 7 2 98.24 1 7 A ILE 8 2 97.73 1 8 A VAL 9 2 98.27 1 9 A TRP 10 2 96.37 1 10 A CYS 11 2 98.15 1 11 A TRP 12 2 95.99 1 12 A GLY 13 2 98.45 1 13 A LEU 14 2 97.02 1 14 A LEU 15 2 96.35 1 15 A SER 16 2 90.85 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 LEU . 3 A 3 A 4 1 n ALA . 4 A 4 A 5 1 n ILE . 5 A 5 A 6 1 n GLY . 6 A 6 A 7 1 n VAL . 7 A 7 A 8 1 n ILE . 8 A 8 A 9 1 n VAL . 9 A 9 A 10 1 n TRP . 10 A 10 A 11 1 n CYS . 11 A 11 A 12 1 n TRP . 12 A 12 A 13 1 n GLY . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n LEU . 15 A 15 A 16 1 n SER . 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 ? -2.084 9.697 7.649 1.00 95.07 1 A 1 ATOM 2 C CA . MET A 1 1 ? -2.098 8.670 6.596 1.00 96.70 1 A 1 ATOM 3 C C . MET A 1 1 ? -0.701 8.089 6.386 1.00 97.55 1 A 1 ATOM 4 O O . MET A 1 1 ? -0.110 8.234 5.314 1.00 96.69 1 A 1 ATOM 5 C CB . MET A 1 1 ? -2.573 9.278 5.280 1.00 94.31 1 A 1 ATOM 6 C CG . MET A 1 1 ? -3.958 9.878 5.388 1.00 89.35 1 A 1 ATOM 7 S SD . MET A 1 1 ? -4.421 10.747 3.882 1.00 88.64 1 A 1 ATOM 8 C CE . MET A 1 1 ? -5.999 11.414 4.373 1.00 79.77 1 A 1 ATOM 9 N N . LEU A 1 2 ? -0.180 7.453 7.406 1.00 95.13 2 A 1 ATOM 10 C CA . LEU A 1 2 ? 1.156 6.865 7.341 1.00 97.30 2 A 1 ATOM 11 C C . LEU A 1 2 ? 1.090 5.355 7.145 1.00 98.19 2 A 1 ATOM 12 O O . LEU A 1 2 ? 1.704 4.804 6.233 1.00 97.75 2 A 1 ATOM 13 C CB . LEU A 1 2 ? 1.916 7.187 8.631 1.00 96.68 2 A 1 ATOM 14 C CG . LEU A 1 2 ? 2.266 8.663 8.782 1.00 94.38 2 A 1 ATOM 15 C CD1 . LEU A 1 2 ? 2.622 8.978 10.227 1.00 91.74 2 A 1 ATOM 16 C CD2 . LEU A 1 2 ? 3.433 9.016 7.867 1.00 90.49 2 A 1 ATOM 17 N N . LEU A 1 3 ? 0.345 4.680 8.010 1.00 97.15 3 A 1 ATOM 18 C CA . LEU A 1 3 ? 0.196 3.226 7.924 1.00 97.82 3 A 1 ATOM 19 C C . LEU A 1 3 ? -0.614 2.816 6.700 1.00 98.30 3 A 1 ATOM 20 O O . LEU A 1 3 ? -0.290 1.840 6.026 1.00 98.15 3 A 1 ATOM 21 C CB . LEU A 1 3 ? -0.479 2.702 9.194 1.00 97.62 3 A 1 ATOM 22 C CG . LEU A 1 3 ? 0.501 2.290 10.282 1.00 95.39 3 A 1 ATOM 23 C CD1 . LEU A 1 3 ? 0.075 2.840 11.633 1.00 92.62 3 A 1 ATOM 24 C CD2 . LEU A 1 3 ? 0.621 0.780 10.336 1.00 92.12 3 A 1 ATOM 25 N N . ALA A 1 4 ? -1.672 3.552 6.410 1.00 97.98 4 A 1 ATOM 26 C CA . ALA A 1 4 ? -2.537 3.261 5.268 1.00 98.41 4 A 1 ATOM 27 C C . ALA A 1 4 ? -1.760 3.287 3.957 1.00 98.61 4 A 1 ATOM 28 O O . ALA A 1 4 ? -1.960 2.439 3.091 1.00 98.40 4 A 1 ATOM 29 C CB . ALA A 1 4 ? -3.683 4.263 5.215 1.00 98.09 4 A 1 ATOM 30 N N . ILE A 1 5 ? -0.878 4.263 3.808 1.00 98.36 5 A 1 ATOM 31 C CA . ILE A 1 5 ? -0.078 4.402 2.591 1.00 98.36 5 A 1 ATOM 32 C C . ILE A 1 5 ? 0.778 3.164 2.352 1.00 98.48 5 A 1 ATOM 33 O O . ILE A 1 5 ? 0.824 2.627 1.244 1.00 98.27 5 A 1 ATOM 34 C CB . ILE A 1 5 ? 0.830 5.640 2.672 1.00 98.11 5 A 1 ATOM 35 C CG1 . ILE A 1 5 ? -0.009 6.910 2.785 1.00 96.66 5 A 1 ATOM 36 C CG2 . ILE A 1 5 ? 1.720 5.711 1.430 1.00 96.35 5 A 1 ATOM 37 C CD1 . ILE A 1 5 ? 0.811 8.122 3.181 1.00 93.68 5 A 1 ATOM 38 N N . GLY A 1 6 ? 1.457 2.715 3.393 1.00 98.40 6 A 1 ATOM 39 C CA . GLY A 1 6 ? 2.309 1.535 3.282 1.00 98.34 6 A 1 ATOM 40 C C . GLY A 1 6 ? 1.527 0.295 2.901 1.00 98.54 6 A 1 ATOM 41 O O . GLY A 1 6 ? 1.947 -0.490 2.052 1.00 98.28 6 A 1 ATOM 42 N N . VAL A 1 7 ? 0.382 0.115 3.531 1.00 98.61 7 A 1 ATOM 43 C CA . VAL A 1 7 ? -0.478 -1.039 3.262 1.00 98.67 7 A 1 ATOM 44 C C . VAL A 1 7 ? -0.996 -1.022 1.827 1.00 98.74 7 A 1 ATOM 45 O O . VAL A 1 7 ? -1.025 -2.052 1.152 1.00 98.56 7 A 1 ATOM 46 C CB . VAL A 1 7 ? -1.675 -1.070 4.225 1.00 98.49 7 A 1 ATOM 47 C CG1 . VAL A 1 7 ? -2.577 -2.260 3.927 1.00 97.44 7 A 1 ATOM 48 C CG2 . VAL A 1 7 ? -1.190 -1.126 5.665 1.00 97.19 7 A 1 ATOM 49 N N . ILE A 1 8 ? -1.418 0.144 1.371 1.00 98.60 8 A 1 ATOM 50 C CA . ILE A 1 8 ? -1.943 0.294 0.015 1.00 98.51 8 A 1 ATOM 51 C C . ILE A 1 8 ? -0.887 -0.061 -1.021 1.00 98.50 8 A 1 ATOM 52 O O . ILE A 1 8 ? -1.154 -0.798 -1.975 1.00 98.27 8 A 1 ATOM 53 C CB . ILE A 1 8 ? -2.430 1.730 -0.229 1.00 98.35 8 A 1 ATOM 54 C CG1 . ILE A 1 8 ? -3.627 2.047 0.662 1.00 97.54 8 A 1 ATOM 55 C CG2 . ILE A 1 8 ? -2.822 1.904 -1.700 1.00 97.32 8 A 1 ATOM 56 C CD1 . ILE A 1 8 ? -3.916 3.527 0.756 1.00 94.74 8 A 1 ATOM 57 N N . VAL A 1 9 ? 0.308 0.466 -0.845 1.00 98.63 9 A 1 ATOM 58 C CA . VAL A 1 9 ? 1.409 0.198 -1.772 1.00 98.59 9 A 1 ATOM 59 C C . VAL A 1 9 ? 1.741 -1.289 -1.794 1.00 98.62 9 A 1 ATOM 60 O O . VAL A 1 9 ? 1.989 -1.868 -2.856 1.00 98.48 9 A 1 ATOM 61 C CB . VAL A 1 9 ? 2.664 0.993 -1.378 1.00 98.39 9 A 1 ATOM 62 C CG1 . VAL A 1 9 ? 3.822 0.665 -2.305 1.00 97.59 9 A 1 ATOM 63 C CG2 . VAL A 1 9 ? 2.375 2.483 -1.403 1.00 97.59 9 A 1 ATOM 64 N N . TRP A 1 10 ? 1.758 -1.894 -0.620 1.00 98.44 10 A 1 ATOM 65 C CA . TRP A 1 10 ? 2.050 -3.320 -0.503 1.00 98.34 10 A 1 ATOM 66 C C . TRP A 1 10 ? 1.005 -4.149 -1.236 1.00 98.47 10 A 1 ATOM 67 O O . TRP A 1 10 ? 1.338 -5.085 -1.966 1.00 98.22 10 A 1 ATOM 68 C CB . TRP A 1 10 ? 2.089 -3.724 0.968 1.00 98.12 10 A 1 ATOM 69 C CG . TRP A 1 10 ? 2.031 -5.207 1.159 1.00 97.26 10 A 1 ATOM 70 C CD1 . TRP A 1 10 ? 1.029 -5.907 1.756 1.00 95.42 10 A 1 ATOM 71 C CD2 . TRP A 1 10 ? 2.999 -6.179 0.726 1.00 96.55 10 A 1 ATOM 72 N NE1 . TRP A 1 10 ? 1.315 -7.252 1.725 1.00 94.48 10 A 1 ATOM 73 C CE2 . TRP A 1 10 ? 2.516 -7.458 1.101 1.00 96.06 10 A 1 ATOM 74 C CE3 . TRP A 1 10 ? 4.224 -6.094 0.058 1.00 95.29 10 A 1 ATOM 75 C CZ2 . TRP A 1 10 ? 3.228 -8.629 0.831 1.00 95.48 10 A 1 ATOM 76 C CZ3 . TRP A 1 10 ? 4.931 -7.265 -0.209 1.00 93.37 10 A 1 ATOM 77 C CH2 . TRP A 1 10 ? 4.427 -8.518 0.177 1.00 93.74 10 A 1 ATOM 78 N N . CYS A 1 11 ? -0.264 -3.823 -1.039 1.00 98.59 11 A 1 ATOM 79 C CA . CYS A 1 11 ? -1.359 -4.541 -1.687 1.00 98.55 11 A 1 ATOM 80 C C . CYS A 1 11 ? -1.274 -4.417 -3.204 1.00 98.56 11 A 1 ATOM 81 O O . CYS A 1 11 ? -1.505 -5.381 -3.924 1.00 98.16 11 A 1 ATOM 82 C CB . CYS A 1 11 ? -2.703 -3.994 -1.205 1.00 98.31 11 A 1 ATOM 83 S SG . CYS A 1 11 ? -3.097 -4.490 0.484 1.00 96.74 11 A 1 ATOM 84 N N . TRP A 1 12 ? -0.952 -3.217 -3.683 1.00 98.37 12 A 1 ATOM 85 C CA . TRP A 1 12 ? -0.829 -2.981 -5.119 1.00 98.34 12 A 1 ATOM 86 C C . TRP A 1 12 ? 0.314 -3.787 -5.712 1.00 98.53 12 A 1 ATOM 87 O O . TRP A 1 12 ? 0.194 -4.354 -6.795 1.00 98.28 12 A 1 ATOM 88 C CB . TRP A 1 12 ? -0.604 -1.492 -5.379 1.00 98.07 12 A 1 ATOM 89 C CG . TRP A 1 12 ? -1.840 -0.818 -5.873 1.00 97.16 12 A 1 ATOM 90 C CD1 . TRP A 1 12 ? -2.611 0.071 -5.200 1.00 94.94 12 A 1 ATOM 91 C CD2 . TRP A 1 12 ? -2.452 -0.983 -7.160 1.00 96.26 12 A 1 ATOM 92 N NE1 . TRP A 1 12 ? -3.664 0.469 -5.984 1.00 94.09 12 A 1 ATOM 93 C CE2 . TRP A 1 12 ? -3.595 -0.162 -7.196 1.00 95.69 12 A 1 ATOM 94 C CE3 . TRP A 1 12 ? -2.143 -1.749 -8.289 1.00 94.62 12 A 1 ATOM 95 C CZ2 . TRP A 1 12 ? -4.423 -0.090 -8.314 1.00 95.01 12 A 1 ATOM 96 C CZ3 . TRP A 1 12 ? -2.963 -1.677 -9.402 1.00 92.19 12 A 1 ATOM 97 C CH2 . TRP A 1 12 ? -4.091 -0.854 -9.407 1.00 92.34 12 A 1 ATOM 98 N N . GLY A 1 13 ? 1.423 -3.854 -5.002 1.00 98.49 13 A 1 ATOM 99 C CA . GLY A 1 13 ? 2.585 -4.600 -5.464 1.00 98.46 13 A 1 ATOM 100 C C . GLY A 1 13 ? 2.309 -6.081 -5.592 1.00 98.59 13 A 1 ATOM 101 O O . GLY A 1 13 ? 2.678 -6.705 -6.587 1.00 98.28 13 A 1 ATOM 102 N N . LEU A 1 14 ? 1.657 -6.668 -4.591 1.00 98.28 14 A 1 ATOM 103 C CA . LEU A 1 14 ? 1.336 -8.093 -4.613 1.00 98.27 14 A 1 ATOM 104 C C . LEU A 1 14 ? 0.203 -8.383 -5.589 1.00 98.34 14 A 1 ATOM 105 O O . LEU A 1 14 ? 0.115 -9.484 -6.139 1.00 97.63 14 A 1 ATOM 106 C CB . LEU A 1 14 ? 0.947 -8.560 -3.204 1.00 98.03 14 A 1 ATOM 107 C CG . LEU A 1 14 ? -0.474 -8.176 -2.789 1.00 96.77 14 A 1 ATOM 108 C CD1 . LEU A 1 14 ? -1.480 -9.233 -3.243 1.00 94.94 14 A 1 ATOM 109 C CD2 . LEU A 1 14 ? -0.549 -8.027 -1.276 1.00 93.92 14 A 1 ATOM 110 N N . LEU A 1 15 ? -0.689 -7.421 -5.782 1.00 98.11 15 A 1 ATOM 111 C CA . LEU A 1 15 ? -1.825 -7.570 -6.689 1.00 97.81 15 A 1 ATOM 112 C C . LEU A 1 15 ? -1.358 -7.578 -8.137 1.00 97.73 15 A 1 ATOM 113 O O . LEU A 1 15 ? -1.749 -8.448 -8.924 1.00 96.83 15 A 1 ATOM 114 C CB . LEU A 1 15 ? -2.834 -6.436 -6.472 1.00 97.40 15 A 1 ATOM 115 C CG . LEU A 1 15 ? -4.197 -6.627 -7.136 1.00 96.42 15 A 1 ATOM 116 C CD1 . LEU A 1 15 ? -4.092 -6.533 -8.646 1.00 94.24 15 A 1 ATOM 117 C CD2 . LEU A 1 15 ? -4.780 -7.976 -6.728 1.00 92.26 15 A 1 ATOM 118 N N . SER A 1 16 ? -0.537 -6.601 -8.501 1.00 96.30 16 A 1 ATOM 119 C CA . SER A 1 16 ? -0.028 -6.483 -9.870 1.00 94.81 16 A 1 ATOM 120 C C . SER A 1 16 ? 0.860 -7.668 -10.222 1.00 92.85 16 A 1 ATOM 121 O O . SER A 1 16 ? 0.625 -8.316 -11.254 1.00 87.85 16 A 1 ATOM 122 C CB . SER A 1 16 ? 0.752 -5.180 -10.033 1.00 91.62 16 A 1 ATOM 123 O OG . SER A 1 16 ? -0.105 -4.066 -9.940 1.00 85.73 16 A 1 ATOM 124 O OXT . SER A 1 16 ? 1.795 -7.955 -9.475 1.00 86.80 16 A 1 #