# 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_spkb35874 # _entry.id spkb35874 # 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" "C5 H10 N2 O3" 146.144 GLN y GLUTAMINE C(CC(=O)N)[C@@H](C(=O)O)N ? "L-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" "C9 H11 N O2" 165.189 PHE y PHENYLALANINE c1ccc(cc1)C[C@@H](C(=O)O)N ? "L-PEPTIDE LINKING" "C9 H11 N O3" 181.189 TYR y TYROSINE c1cc(ccc1C[C@@H](C(=O)O)N)O ? "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 ILE 2 1 n ILE 3 1 n ALA 4 1 n PHE 5 1 n PHE 6 1 n LEU 7 1 n LEU 8 1 n ILE 9 1 n GLN 10 1 n CYS 11 1 n VAL 12 1 n TYR 13 1 n CYS 14 # _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 @ 2025-07-02 12:33:26)" _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 95.31 _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 88.69 1 1 A ILE 2 2 93.93 1 2 A ILE 3 2 95.72 1 3 A ALA 4 2 97.81 1 4 A PHE 5 2 95.18 1 5 A PHE 6 2 95.69 1 6 A LEU 7 2 96.77 1 7 A LEU 8 2 96.52 1 8 A ILE 9 2 96.79 1 9 A GLN 10 2 95.73 1 10 A CYS 11 2 97.32 1 11 A VAL 12 2 97.14 1 12 A TYR 13 2 95.23 1 13 A CYS 14 2 93.20 1 14 # _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 ILE . 2 A 2 A 3 1 n ILE . 3 A 3 A 4 1 n ALA . 4 A 4 A 5 1 n PHE . 5 A 5 A 6 1 n PHE . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n ILE . 9 A 9 A 10 1 n GLN . 10 A 10 A 11 1 n CYS . 11 A 11 A 12 1 n VAL . 12 A 12 A 13 1 n TYR . 13 A 13 A 14 1 n CYS . 14 A 14 # _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 ? -2.537 -8.818 2.884 1.00 93.78 1 A 1 ATOM 2 C CA . MET A 1 1 ? -1.746 -8.182 1.817 1.00 93.66 1 A 1 ATOM 3 C C . MET A 1 1 ? -0.929 -7.020 2.373 1.00 93.24 1 A 1 ATOM 4 O O . MET A 1 1 ? -1.479 -5.976 2.716 1.00 90.81 1 A 1 ATOM 5 C CB . MET A 1 1 ? -2.662 -7.668 0.711 1.00 90.77 1 A 1 ATOM 6 C CG . MET A 1 1 ? -3.321 -8.781 -0.081 1.00 85.56 1 A 1 ATOM 7 S SD . MET A 1 1 ? -2.134 -9.679 -1.061 1.00 84.89 1 A 1 ATOM 8 C CE . MET A 1 1 ? -3.219 -10.784 -1.957 1.00 76.84 1 A 1 ATOM 9 N N . ILE A 1 2 ? 0.375 -7.227 2.443 1.00 94.84 2 A 1 ATOM 10 C CA . ILE A 1 2 ? 1.273 -6.211 2.976 1.00 96.02 2 A 1 ATOM 11 C C . ILE A 1 2 ? 1.465 -5.076 1.979 1.00 96.93 2 A 1 ATOM 12 O O . ILE A 1 2 ? 1.652 -3.921 2.360 1.00 96.58 2 A 1 ATOM 13 C CB . ILE A 1 2 ? 2.628 -6.828 3.329 1.00 95.34 2 A 1 ATOM 14 C CG1 . ILE A 1 2 ? 2.439 -8.024 4.255 1.00 92.48 2 A 1 ATOM 15 C CG2 . ILE A 1 2 ? 3.518 -5.788 3.985 1.00 91.54 2 A 1 ATOM 16 C CD1 . ILE A 1 2 ? 3.715 -8.792 4.473 1.00 87.71 2 A 1 ATOM 17 N N . ILE A 1 3 ? 1.424 -5.419 0.697 1.00 97.07 3 A 1 ATOM 18 C CA . ILE A 1 3 ? 1.599 -4.425 -0.359 1.00 97.01 3 A 1 ATOM 19 C C . ILE A 1 3 ? 0.503 -3.372 -0.294 1.00 97.25 3 A 1 ATOM 20 O O . ILE A 1 3 ? 0.757 -2.180 -0.460 1.00 97.05 3 A 1 ATOM 21 C CB . ILE A 1 3 ? 1.605 -5.089 -1.745 1.00 96.76 3 A 1 ATOM 22 C CG1 . ILE A 1 3 ? 2.719 -6.126 -1.830 1.00 94.92 3 A 1 ATOM 23 C CG2 . ILE A 1 3 ? 1.784 -4.033 -2.826 1.00 94.30 3 A 1 ATOM 24 C CD1 . ILE A 1 3 ? 2.657 -6.953 -3.095 1.00 91.36 3 A 1 ATOM 25 N N . ALA A 1 4 ? -0.720 -3.823 -0.070 1.00 97.73 4 A 1 ATOM 26 C CA . ALA A 1 4 ? -1.856 -2.909 0.030 1.00 97.87 4 A 1 ATOM 27 C C . ALA A 1 4 ? -1.685 -1.970 1.213 1.00 98.10 4 A 1 ATOM 28 O O . ALA A 1 4 ? -2.064 -0.802 1.155 1.00 97.86 4 A 1 ATOM 29 C CB . ALA A 1 4 ? -3.149 -3.698 0.160 1.00 97.47 4 A 1 ATOM 30 N N . PHE A 1 5 ? -1.114 -2.494 2.266 1.00 97.36 5 A 1 ATOM 31 C CA . PHE A 1 5 ? -0.855 -1.708 3.463 1.00 97.31 5 A 1 ATOM 32 C C . PHE A 1 5 ? 0.191 -0.641 3.171 1.00 97.71 5 A 1 ATOM 33 O O . PHE A 1 5 ? 0.069 0.506 3.595 1.00 97.48 5 A 1 ATOM 34 C CB . PHE A 1 5 ? -0.384 -2.629 4.584 1.00 97.06 5 A 1 ATOM 35 C CG . PHE A 1 5 ? -0.415 -1.978 5.939 1.00 95.13 5 A 1 ATOM 36 C CD1 . PHE A 1 5 ? -1.059 -0.775 6.138 1.00 92.95 5 A 1 ATOM 37 C CD2 . PHE A 1 5 ? 0.193 -2.594 7.014 1.00 93.59 5 A 1 ATOM 38 C CE1 . PHE A 1 5 ? -1.092 -0.178 7.383 1.00 92.90 5 A 1 ATOM 39 C CE2 . PHE A 1 5 ? 0.163 -2.008 8.267 1.00 92.25 5 A 1 ATOM 40 C CZ . PHE A 1 5 ? -0.475 -0.798 8.444 1.00 93.19 5 A 1 ATOM 41 N N . PHE A 1 6 ? 1.216 -1.034 2.441 1.00 97.66 6 A 1 ATOM 42 C CA . PHE A 1 6 ? 2.276 -0.114 2.052 1.00 97.78 6 A 1 ATOM 43 C C . PHE A 1 6 ? 1.727 1.011 1.181 1.00 98.13 6 A 1 ATOM 44 O O . PHE A 1 6 ? 2.080 2.177 1.356 1.00 97.95 6 A 1 ATOM 45 C CB . PHE A 1 6 ? 3.363 -0.873 1.303 1.00 97.54 6 A 1 ATOM 46 C CG . PHE A 1 6 ? 4.457 0.021 0.808 1.00 96.12 6 A 1 ATOM 47 C CD1 . PHE A 1 6 ? 5.303 0.652 1.698 1.00 93.62 6 A 1 ATOM 48 C CD2 . PHE A 1 6 ? 4.624 0.230 -0.546 1.00 94.33 6 A 1 ATOM 49 C CE1 . PHE A 1 6 ? 6.308 1.482 1.247 1.00 93.20 6 A 1 ATOM 50 C CE2 . PHE A 1 6 ? 5.630 1.063 -1.005 1.00 92.99 6 A 1 ATOM 51 C CZ . PHE A 1 6 ? 6.470 1.686 -0.108 1.00 93.27 6 A 1 ATOM 52 N N . LEU A 1 7 ? 0.864 0.638 0.236 1.00 97.67 7 A 1 ATOM 53 C CA . LEU A 1 7 ? 0.252 1.614 -0.658 1.00 97.87 7 A 1 ATOM 54 C C . LEU A 1 7 ? -0.611 2.595 0.117 1.00 98.17 7 A 1 ATOM 55 O O . LEU A 1 7 ? -0.687 3.774 -0.233 1.00 98.07 7 A 1 ATOM 56 C CB . LEU A 1 7 ? -0.595 0.894 -1.706 1.00 97.80 7 A 1 ATOM 57 C CG . LEU A 1 7 ? 0.212 0.286 -2.843 1.00 95.32 7 A 1 ATOM 58 C CD1 . LEU A 1 7 ? -0.654 -0.642 -3.675 1.00 94.35 7 A 1 ATOM 59 C CD2 . LEU A 1 7 ? 0.790 1.385 -3.721 1.00 94.88 7 A 1 ATOM 60 N N . LEU A 1 8 ? -1.257 2.096 1.139 1.00 98.08 8 A 1 ATOM 61 C CA . LEU A 1 8 ? -2.110 2.932 1.975 1.00 98.01 8 A 1 ATOM 62 C C . LEU A 1 8 ? -1.288 4.033 2.634 1.00 98.08 8 A 1 ATOM 63 O O . LEU A 1 8 ? -1.735 5.175 2.740 1.00 97.82 8 A 1 ATOM 64 C CB . LEU A 1 8 ? -2.800 2.078 3.037 1.00 97.81 8 A 1 ATOM 65 C CG . LEU A 1 8 ? -3.847 2.811 3.867 1.00 95.25 8 A 1 ATOM 66 C CD1 . LEU A 1 8 ? -5.025 3.227 2.997 1.00 93.23 8 A 1 ATOM 67 C CD2 . LEU A 1 8 ? -4.328 1.935 5.012 1.00 93.89 8 A 1 ATOM 68 N N . ILE A 1 9 ? -0.092 3.677 3.052 1.00 98.25 9 A 1 ATOM 69 C CA . ILE A 1 9 ? 0.808 4.641 3.676 1.00 98.08 9 A 1 ATOM 70 C C . ILE A 1 9 ? 1.255 5.682 2.660 1.00 98.13 9 A 1 ATOM 71 O O . ILE A 1 9 ? 1.370 6.868 2.971 1.00 97.78 9 A 1 ATOM 72 C CB . ILE A 1 9 ? 2.034 3.933 4.273 1.00 97.76 9 A 1 ATOM 73 C CG1 . ILE A 1 9 ? 1.598 2.862 5.273 1.00 95.92 9 A 1 ATOM 74 C CG2 . ILE A 1 9 ? 2.951 4.948 4.949 1.00 95.98 9 A 1 ATOM 75 C CD1 . ILE A 1 9 ? 0.810 3.423 6.437 1.00 92.43 9 A 1 ATOM 76 N N . GLN A 1 10 ? 1.510 5.220 1.432 1.00 98.13 10 A 1 ATOM 77 C CA . GLN A 1 10 ? 1.936 6.112 0.359 1.00 97.98 10 A 1 ATOM 78 C C . GLN A 1 10 ? 0.873 7.154 0.061 1.00 98.10 10 A 1 ATOM 79 O O . GLN A 1 10 ? 1.188 8.293 -0.280 1.00 97.48 10 A 1 ATOM 80 C CB . GLN A 1 10 ? 2.248 5.310 -0.900 1.00 97.61 10 A 1 ATOM 81 C CG . GLN A 1 10 ? 3.389 4.336 -0.727 1.00 95.56 10 A 1 ATOM 82 C CD . GLN A 1 10 ? 4.666 5.039 -0.332 1.00 94.98 10 A 1 ATOM 83 O OE1 . GLN A 1 10 ? 4.990 5.139 0.845 1.00 91.57 10 A 1 ATOM 84 N NE2 . GLN A 1 10 ? 5.392 5.545 -1.307 1.00 90.17 10 A 1 ATOM 85 N N . CYS A 1 11 ? -0.393 6.766 0.190 1.00 97.90 11 A 1 ATOM 86 C CA . CYS A 1 11 ? -1.506 7.675 -0.051 1.00 97.89 11 A 1 ATOM 87 C C . CYS A 1 11 ? -1.446 8.880 0.878 1.00 98.05 11 A 1 ATOM 88 O O . CYS A 1 11 ? -1.853 9.978 0.508 1.00 97.36 11 A 1 ATOM 89 C CB . CYS A 1 11 ? -2.843 6.949 0.134 1.00 97.34 11 A 1 ATOM 90 S SG . CYS A 1 11 ? -3.485 6.236 -1.384 1.00 95.35 11 A 1 ATOM 91 N N . VAL A 1 12 ? -0.939 8.655 2.067 1.00 97.92 12 A 1 ATOM 92 C CA . VAL A 1 12 ? -0.812 9.730 3.042 1.00 97.94 12 A 1 ATOM 93 C C . VAL A 1 12 ? 0.345 10.649 2.673 1.00 98.10 12 A 1 ATOM 94 O O . VAL A 1 12 ? 0.333 11.841 2.995 1.00 97.67 12 A 1 ATOM 95 C CB . VAL A 1 12 ? -0.607 9.169 4.459 1.00 97.60 12 A 1 ATOM 96 C CG1 . VAL A 1 12 ? -0.693 10.279 5.489 1.00 95.32 12 A 1 ATOM 97 C CG2 . VAL A 1 12 ? -1.637 8.094 4.768 1.00 95.46 12 A 1 ATOM 98 N N . TYR A 1 13 ? 1.342 10.077 2.004 1.00 97.78 13 A 1 ATOM 99 C CA . TYR A 1 13 ? 2.515 10.837 1.602 1.00 97.54 13 A 1 ATOM 100 C C . TYR A 1 13 ? 2.375 11.382 0.182 1.00 97.30 13 A 1 ATOM 101 O O . TYR A 1 13 ? 3.259 12.094 -0.297 1.00 96.19 13 A 1 ATOM 102 C CB . TYR A 1 13 ? 3.764 9.952 1.697 1.00 97.15 13 A 1 ATOM 103 C CG . TYR A 1 13 ? 3.999 9.400 3.090 1.00 95.61 13 A 1 ATOM 104 C CD1 . TYR A 1 13 ? 3.731 10.167 4.215 1.00 93.67 13 A 1 ATOM 105 C CD2 . TYR A 1 13 ? 4.505 8.119 3.266 1.00 93.66 13 A 1 ATOM 106 C CE1 . TYR A 1 13 ? 3.954 9.669 5.484 1.00 93.48 13 A 1 ATOM 107 C CE2 . TYR A 1 13 ? 4.737 7.614 4.536 1.00 93.35 13 A 1 ATOM 108 C CZ . TYR A 1 13 ? 4.456 8.393 5.641 1.00 94.25 13 A 1 ATOM 109 O OH . TYR A 1 13 ? 4.672 7.896 6.898 1.00 92.72 13 A 1 ATOM 110 N N . CYS A 1 14 ? 1.258 11.029 -0.475 1.00 96.30 14 A 1 ATOM 111 C CA . CYS A 1 14 ? 0.998 11.481 -1.842 1.00 95.30 14 A 1 ATOM 112 C C . CYS A 1 14 ? 0.714 12.981 -1.843 1.00 94.67 14 A 1 ATOM 113 O O . CYS A 1 14 ? 1.175 13.681 -2.748 1.00 93.17 14 A 1 ATOM 114 C CB . CYS A 1 14 ? -0.176 10.712 -2.450 1.00 92.99 14 A 1 ATOM 115 S SG . CYS A 1 14 ? 0.251 9.052 -3.001 1.00 90.85 14 A 1 ATOM 116 O OXT . CYS A 1 14 ? -0.014 13.448 -0.946 1.00 89.11 14 A 1 #