# 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_spkb10041 # _entry.id spkb10041 # 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" "C6 H15 N4 O2" 175.209 ARG y ARGININE C(C[C@@H](C(=O)O)N)CNC(=[NH2+])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" "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 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 ARG 2 1 n GLY 3 1 n GLY 4 1 n VAL 5 1 n LEU 6 1 n LEU 7 1 n VAL 8 1 n LEU 9 1 n LEU 10 1 n LEU 11 1 n CYS 12 1 n VAL 13 1 n ALA 14 1 n ALA 15 1 n GLN 16 1 n CYS 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 @ 2025-07-05 04:27:05)" _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 94.30 _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 85.16 1 1 A ARG 2 2 84.97 1 2 A GLY 3 2 95.88 1 3 A GLY 4 2 97.03 1 4 A VAL 5 2 96.67 1 5 A LEU 6 2 96.31 1 6 A LEU 7 2 96.19 1 7 A VAL 8 2 97.56 1 8 A LEU 9 2 96.04 1 9 A LEU 10 2 96.55 1 10 A LEU 11 2 96.31 1 11 A CYS 12 2 97.22 1 12 A VAL 13 2 97.59 1 13 A ALA 14 2 98.16 1 14 A ALA 15 2 97.91 1 15 A GLN 16 2 92.75 1 16 A CYS 17 2 90.80 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 ARG . 2 A 2 A 3 1 n GLY . 3 A 3 A 4 1 n GLY . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n VAL . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n CYS . 12 A 12 A 13 1 n VAL . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n GLN . 16 A 16 A 17 1 n CYS . 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 ? 5.826 7.089 11.745 1.00 91.18 1 A 1 ATOM 2 C CA . MET A 1 1 ? 4.378 7.354 11.648 1.00 91.19 1 A 1 ATOM 3 C C . MET A 1 1 ? 3.677 6.218 10.908 1.00 92.37 1 A 1 ATOM 4 O O . MET A 1 1 ? 4.211 5.685 9.939 1.00 88.18 1 A 1 ATOM 5 C CB . MET A 1 1 ? 4.140 8.675 10.925 1.00 87.47 1 A 1 ATOM 6 C CG . MET A 1 1 ? 4.691 9.840 11.725 1.00 83.68 1 A 1 ATOM 7 S SD . MET A 1 1 ? 4.385 11.434 10.969 1.00 79.25 1 A 1 ATOM 8 C CE . MET A 1 1 ? 5.571 11.411 9.659 1.00 67.97 1 A 1 ATOM 9 N N . ARG A 1 2 ? 2.499 5.842 11.385 1.00 91.76 2 A 1 ATOM 10 C CA . ARG A 1 2 ? 1.751 4.709 10.831 1.00 94.52 2 A 1 ATOM 11 C C . ARG A 1 2 ? 1.083 5.022 9.495 1.00 95.79 2 A 1 ATOM 12 O O . ARG A 1 2 ? 0.754 4.110 8.739 1.00 94.27 2 A 1 ATOM 13 C CB . ARG A 1 2 ? 0.716 4.231 11.859 1.00 92.18 2 A 1 ATOM 14 C CG . ARG A 1 2 ? -0.467 5.154 12.037 1.00 85.53 2 A 1 ATOM 15 C CD . ARG A 1 2 ? -0.104 6.491 12.668 1.00 83.83 2 A 1 ATOM 16 N NE . ARG A 1 2 ? 0.278 7.468 11.641 1.00 78.45 2 A 1 ATOM 17 C CZ . ARG A 1 2 ? 0.416 8.766 11.877 1.00 77.31 2 A 1 ATOM 18 N NH1 . ARG A 1 2 ? 0.193 9.272 13.076 1.00 70.47 2 A 1 ATOM 19 N NH2 . ARG A 1 2 ? 0.786 9.558 10.906 1.00 70.60 2 A 1 ATOM 20 N N . GLY A 1 3 ? 0.859 6.289 9.215 1.00 94.54 3 A 1 ATOM 21 C CA . GLY A 1 3 ? 0.184 6.676 7.975 1.00 96.02 3 A 1 ATOM 22 C C . GLY A 1 3 ? 0.863 6.128 6.731 1.00 97.01 3 A 1 ATOM 23 O O . GLY A 1 3 ? 0.215 5.574 5.849 1.00 95.93 3 A 1 ATOM 24 N N . GLY A 1 4 ? 2.189 6.283 6.669 1.00 96.33 4 A 1 ATOM 25 C CA . GLY A 1 4 ? 2.948 5.799 5.515 1.00 97.03 4 A 1 ATOM 26 C C . GLY A 1 4 ? 2.831 4.298 5.331 1.00 97.63 4 A 1 ATOM 27 O O . GLY A 1 4 ? 2.634 3.809 4.221 1.00 97.13 4 A 1 ATOM 28 N N . VAL A 1 5 ? 2.942 3.551 6.420 1.00 97.51 5 A 1 ATOM 29 C CA . VAL A 1 5 ? 2.854 2.090 6.375 1.00 97.82 5 A 1 ATOM 30 C C . VAL A 1 5 ? 1.488 1.649 5.854 1.00 98.09 5 A 1 ATOM 31 O O . VAL A 1 5 ? 1.390 0.762 5.005 1.00 97.70 5 A 1 ATOM 32 C CB . VAL A 1 5 ? 3.096 1.482 7.763 1.00 97.28 5 A 1 ATOM 33 C CG1 . VAL A 1 5 ? 2.987 -0.033 7.703 1.00 94.38 5 A 1 ATOM 34 C CG2 . VAL A 1 5 ? 4.462 1.898 8.282 1.00 93.94 5 A 1 ATOM 35 N N . LEU A 1 6 ? 0.441 2.269 6.371 1.00 97.47 6 A 1 ATOM 36 C CA . LEU A 1 6 ? -0.916 1.929 5.949 1.00 97.78 6 A 1 ATOM 37 C C . LEU A 1 6 ? -1.095 2.177 4.455 1.00 98.04 6 A 1 ATOM 38 O O . LEU A 1 6 ? -1.737 1.389 3.760 1.00 97.92 6 A 1 ATOM 39 C CB . LEU A 1 6 ? -1.922 2.771 6.737 1.00 97.70 6 A 1 ATOM 40 C CG . LEU A 1 6 ? -2.005 2.392 8.210 1.00 95.47 6 A 1 ATOM 41 C CD1 . LEU A 1 6 ? -2.909 3.369 8.949 1.00 93.11 6 A 1 ATOM 42 C CD2 . LEU A 1 6 ? -2.526 0.972 8.368 1.00 92.95 6 A 1 ATOM 43 N N . LEU A 1 7 ? -0.521 3.265 3.973 1.00 97.45 7 A 1 ATOM 44 C CA . LEU A 1 7 ? -0.604 3.609 2.556 1.00 97.73 7 A 1 ATOM 45 C C . LEU A 1 7 ? 0.054 2.529 1.703 1.00 98.07 7 A 1 ATOM 46 O O . LEU A 1 7 ? -0.492 2.099 0.689 1.00 98.05 7 A 1 ATOM 47 C CB . LEU A 1 7 ? 0.073 4.963 2.310 1.00 97.60 7 A 1 ATOM 48 C CG . LEU A 1 7 ? -0.900 6.060 1.911 1.00 94.47 7 A 1 ATOM 49 C CD1 . LEU A 1 7 ? -1.502 5.760 0.554 1.00 92.97 7 A 1 ATOM 50 C CD2 . LEU A 1 7 ? -1.984 6.203 2.962 1.00 93.17 7 A 1 ATOM 51 N N . VAL A 1 8 ? 1.236 2.093 2.120 1.00 97.96 8 A 1 ATOM 52 C CA . VAL A 1 8 ? 1.966 1.051 1.399 1.00 98.08 8 A 1 ATOM 53 C C . VAL A 1 8 ? 1.161 -0.244 1.377 1.00 98.25 8 A 1 ATOM 54 O O . VAL A 1 8 ? 1.047 -0.901 0.339 1.00 98.10 8 A 1 ATOM 55 C CB . VAL A 1 8 ? 3.335 0.798 2.046 1.00 97.81 8 A 1 ATOM 56 C CG1 . VAL A 1 8 ? 4.045 -0.357 1.358 1.00 96.41 8 A 1 ATOM 57 C CG2 . VAL A 1 8 ? 4.183 2.057 1.971 1.00 96.31 8 A 1 ATOM 58 N N . LEU A 1 9 ? 0.609 -0.609 2.528 1.00 97.72 9 A 1 ATOM 59 C CA . LEU A 1 9 ? -0.188 -1.830 2.636 1.00 97.79 9 A 1 ATOM 60 C C . LEU A 1 9 ? -1.409 -1.757 1.724 1.00 98.16 9 A 1 ATOM 61 O O . LEU A 1 9 ? -1.717 -2.704 1.005 1.00 98.15 9 A 1 ATOM 62 C CB . LEU A 1 9 ? -0.637 -2.035 4.083 1.00 97.57 9 A 1 ATOM 63 C CG . LEU A 1 9 ? 0.318 -2.904 4.900 1.00 93.84 9 A 1 ATOM 64 C CD1 . LEU A 1 9 ? 1.720 -2.302 4.920 1.00 92.16 9 A 1 ATOM 65 C CD2 . LEU A 1 9 ? -0.205 -3.061 6.319 1.00 92.92 9 A 1 ATOM 66 N N . LEU A 1 10 ? -2.097 -0.627 1.767 1.00 97.85 10 A 1 ATOM 67 C CA . LEU A 1 10 ? -3.287 -0.428 0.943 1.00 97.97 10 A 1 ATOM 68 C C . LEU A 1 10 ? -2.943 -0.534 -0.537 1.00 98.29 10 A 1 ATOM 69 O O . LEU A 1 10 ? -3.651 -1.187 -1.306 1.00 98.20 10 A 1 ATOM 70 C CB . LEU A 1 10 ? -3.887 0.943 1.236 1.00 97.74 10 A 1 ATOM 71 C CG . LEU A 1 10 ? -5.172 1.218 0.462 1.00 94.82 10 A 1 ATOM 72 C CD1 . LEU A 1 10 ? -6.259 0.230 0.869 1.00 93.57 10 A 1 ATOM 73 C CD2 . LEU A 1 10 ? -5.637 2.642 0.717 1.00 93.96 10 A 1 ATOM 74 N N . LEU A 1 11 ? -1.852 0.113 -0.930 1.00 97.98 11 A 1 ATOM 75 C CA . LEU A 1 11 ? -1.407 0.082 -2.320 1.00 98.06 11 A 1 ATOM 76 C C . LEU A 1 11 ? -1.067 -1.343 -2.742 1.00 98.29 11 A 1 ATOM 77 O O . LEU A 1 11 ? -1.419 -1.778 -3.839 1.00 98.08 11 A 1 ATOM 78 C CB . LEU A 1 11 ? -0.179 0.975 -2.477 1.00 97.86 11 A 1 ATOM 79 C CG . LEU A 1 11 ? 0.344 1.033 -3.905 1.00 94.69 11 A 1 ATOM 80 C CD1 . LEU A 1 11 ? -0.676 1.695 -4.821 1.00 92.59 11 A 1 ATOM 81 C CD2 . LEU A 1 11 ? 1.655 1.807 -3.945 1.00 92.95 11 A 1 ATOM 82 N N . CYS A 1 12 ? -0.380 -2.068 -1.866 1.00 97.93 12 A 1 ATOM 83 C CA . CYS A 1 12 ? 0.018 -3.446 -2.146 1.00 97.96 12 A 1 ATOM 84 C C . CYS A 1 12 ? -1.204 -4.336 -2.351 1.00 98.19 12 A 1 ATOM 85 O O . CYS A 1 12 ? -1.258 -5.130 -3.288 1.00 97.82 12 A 1 ATOM 86 C CB . CYS A 1 12 ? 0.871 -3.976 -0.995 1.00 97.50 12 A 1 ATOM 87 S SG . CYS A 1 12 ? 1.758 -5.479 -1.409 1.00 93.92 12 A 1 ATOM 88 N N . VAL A 1 13 ? -2.203 -4.182 -1.481 1.00 98.19 13 A 1 ATOM 89 C CA . VAL A 1 13 ? -3.432 -4.969 -1.583 1.00 98.16 13 A 1 ATOM 90 C C . VAL A 1 13 ? -4.146 -4.670 -2.894 1.00 98.35 13 A 1 ATOM 91 O O . VAL A 1 13 ? -4.619 -5.580 -3.583 1.00 98.10 13 A 1 ATOM 92 C CB . VAL A 1 13 ? -4.368 -4.668 -0.403 1.00 97.74 13 A 1 ATOM 93 C CG1 . VAL A 1 13 ? -5.699 -5.385 -0.586 1.00 96.09 13 A 1 ATOM 94 C CG2 . VAL A 1 13 ? -3.717 -5.097 0.900 1.00 96.49 13 A 1 ATOM 95 N N . ALA A 1 14 ? -4.235 -3.392 -3.234 1.00 98.35 14 A 1 ATOM 96 C CA . ALA A 1 14 ? -4.899 -2.985 -4.470 1.00 98.28 14 A 1 ATOM 97 C C . ALA A 1 14 ? -4.181 -3.557 -5.689 1.00 98.34 14 A 1 ATOM 98 O O . ALA A 1 14 ? -4.819 -3.953 -6.667 1.00 97.85 14 A 1 ATOM 99 C CB . ALA A 1 14 ? -4.945 -1.465 -4.554 1.00 97.96 14 A 1 ATOM 100 N N . ALA A 1 15 ? -2.854 -3.595 -5.627 1.00 98.31 15 A 1 ATOM 101 C CA . ALA A 1 15 ? -2.044 -4.131 -6.721 1.00 98.15 15 A 1 ATOM 102 C C . ALA A 1 15 ? -1.907 -5.648 -6.628 1.00 98.16 15 A 1 ATOM 103 O O . ALA A 1 15 ? -1.369 -6.284 -7.532 1.00 97.20 15 A 1 ATOM 104 C CB . ALA A 1 15 ? -0.662 -3.482 -6.700 1.00 97.71 15 A 1 ATOM 105 N N . GLN A 1 16 ? -2.397 -6.222 -5.550 1.00 97.72 16 A 1 ATOM 106 C CA . GLN A 1 16 ? -2.327 -7.668 -5.302 1.00 97.37 16 A 1 ATOM 107 C C . GLN A 1 16 ? -0.882 -8.161 -5.278 1.00 97.22 16 A 1 ATOM 108 O O . GLN A 1 16 ? -0.458 -8.932 -6.139 1.00 94.23 16 A 1 ATOM 109 C CB . GLN A 1 16 ? -3.121 -8.420 -6.368 1.00 96.59 16 A 1 ATOM 110 C CG . GLN A 1 16 ? -4.594 -8.063 -6.329 1.00 93.05 16 A 1 ATOM 111 C CD . GLN A 1 16 ? -5.398 -8.878 -7.316 1.00 90.01 16 A 1 ATOM 112 O OE1 . GLN A 1 16 ? -4.869 -9.392 -8.290 1.00 85.10 16 A 1 ATOM 113 N NE2 . GLN A 1 16 ? -6.693 -9.012 -7.081 1.00 83.44 16 A 1 ATOM 114 N N . CYS A 1 17 ? -0.126 -7.692 -4.273 1.00 95.31 17 A 1 ATOM 115 C CA . CYS A 1 17 ? 1.275 -8.099 -4.134 1.00 94.28 17 A 1 ATOM 116 C C . CYS A 1 17 ? 1.359 -9.565 -3.711 1.00 92.86 17 A 1 ATOM 117 O O . CYS A 1 17 ? 0.395 -10.080 -3.132 1.00 89.77 17 A 1 ATOM 118 C CB . CYS A 1 17 ? 1.978 -7.222 -3.096 1.00 91.26 17 A 1 ATOM 119 S SG . CYS A 1 17 ? 1.872 -5.453 -3.422 1.00 87.13 17 A 1 ATOM 120 O OXT . CYS A 1 17 ? 2.404 -10.223 -3.918 1.00 85.00 17 A 1 #