# 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_spkb34491 # _entry.id spkb34491 # 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" "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" "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 ALA 2 1 n ARG 3 1 n LEU 4 1 n THR 5 1 n ARG 6 1 n LEU 7 1 n LEU 8 1 n PRO 9 1 n LEU 10 1 n ALA 11 1 n ALA 12 1 n LEU 13 1 n VAL 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 @ 2025-07-03 00:12:22)" _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 92.63 _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 83.85 1 1 A ALA 2 2 93.32 1 2 A ARG 3 2 87.28 1 3 A LEU 4 2 92.81 1 4 A THR 5 2 94.23 1 5 A ARG 6 2 88.99 1 6 A LEU 7 2 95.03 1 7 A LEU 8 2 94.40 1 8 A PRO 9 2 96.76 1 9 A LEU 10 2 93.85 1 10 A ALA 11 2 96.27 1 11 A ALA 12 2 96.96 1 12 A LEU 13 2 94.66 1 13 A VAL 14 2 95.43 1 14 A LEU 15 2 93.93 1 15 A SER 16 2 94.51 1 16 A ALA 17 2 89.95 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 ALA . 2 A 2 A 3 1 n ARG . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n THR . 5 A 5 A 6 1 n ARG . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n PRO . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n VAL . 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 ? -13.725 -2.683 -3.283 1.00 89.71 1 A 1 ATOM 2 C CA . MET A 1 1 ? -12.808 -1.981 -2.364 1.00 91.01 1 A 1 ATOM 3 C C . MET A 1 1 ? -11.345 -2.287 -2.687 1.00 91.80 1 A 1 ATOM 4 O O . MET A 1 1 ? -10.953 -3.445 -2.749 1.00 89.88 1 A 1 ATOM 5 C CB . MET A 1 1 ? -13.105 -2.388 -0.930 1.00 86.27 1 A 1 ATOM 6 C CG . MET A 1 1 ? -13.104 -3.892 -0.734 1.00 80.33 1 A 1 ATOM 7 S SD . MET A 1 1 ? -13.712 -4.367 0.887 1.00 75.88 1 A 1 ATOM 8 C CE . MET A 1 1 ? -15.466 -4.342 0.565 1.00 65.96 1 A 1 ATOM 9 N N . ALA A 1 2 ? -10.547 -1.243 -2.889 1.00 91.36 2 A 1 ATOM 10 C CA . ALA A 1 2 ? -9.130 -1.402 -3.211 1.00 94.18 2 A 1 ATOM 11 C C . ALA A 1 2 ? -8.219 -0.815 -2.127 1.00 95.49 2 A 1 ATOM 12 O O . ALA A 1 2 ? -7.006 -0.761 -2.285 1.00 93.67 2 A 1 ATOM 13 C CB . ALA A 1 2 ? -8.846 -0.744 -4.551 1.00 91.89 2 A 1 ATOM 14 N N . ARG A 1 3 ? -8.811 -0.368 -1.024 1.00 95.55 3 A 1 ATOM 15 C CA . ARG A 1 3 ? -8.045 0.219 0.076 1.00 96.04 3 A 1 ATOM 16 C C . ARG A 1 3 ? -7.291 -0.848 0.871 1.00 96.98 3 A 1 ATOM 17 O O . ARG A 1 3 ? -6.251 -0.561 1.464 1.00 95.86 3 A 1 ATOM 18 C CB . ARG A 1 3 ? -8.966 0.993 1.011 1.00 94.83 3 A 1 ATOM 19 C CG . ARG A 1 3 ? -9.251 2.412 0.529 1.00 89.03 3 A 1 ATOM 20 C CD . ARG A 1 3 ? -10.516 2.455 -0.322 1.00 85.78 3 A 1 ATOM 21 N NE . ARG A 1 3 ? -10.941 3.825 -0.611 1.00 81.10 3 A 1 ATOM 22 C CZ . ARG A 1 3 ? -11.995 4.137 -1.339 1.00 79.79 3 A 1 ATOM 23 N NH1 . ARG A 1 3 ? -12.738 3.192 -1.876 1.00 72.21 3 A 1 ATOM 24 N NH2 . ARG A 1 3 ? -12.320 5.408 -1.536 1.00 72.86 3 A 1 ATOM 25 N N . LEU A 1 4 ? -7.814 -2.051 0.875 1.00 95.68 4 A 1 ATOM 26 C CA . LEU A 1 4 ? -7.184 -3.149 1.608 1.00 95.77 4 A 1 ATOM 27 C C . LEU A 1 4 ? -5.835 -3.529 1.008 1.00 96.33 4 A 1 ATOM 28 O O . LEU A 1 4 ? -4.885 -3.813 1.736 1.00 95.27 4 A 1 ATOM 29 C CB . LEU A 1 4 ? -8.117 -4.363 1.621 1.00 95.44 4 A 1 ATOM 30 C CG . LEU A 1 4 ? -9.029 -4.432 2.837 1.00 91.56 4 A 1 ATOM 31 C CD1 . LEU A 1 4 ? -10.235 -5.313 2.564 1.00 86.62 4 A 1 ATOM 32 C CD2 . LEU A 1 4 ? -8.254 -4.953 4.036 1.00 85.82 4 A 1 ATOM 33 N N . THR A 1 5 ? -5.756 -3.536 -0.320 1.00 96.45 5 A 1 ATOM 34 C CA . THR A 1 5 ? -4.521 -3.895 -1.019 1.00 96.65 5 A 1 ATOM 35 C C . THR A 1 5 ? -3.493 -2.766 -0.966 1.00 96.92 5 A 1 ATOM 36 O O . THR A 1 5 ? -2.325 -2.969 -1.281 1.00 96.03 5 A 1 ATOM 37 C CB . THR A 1 5 ? -4.814 -4.276 -2.480 1.00 95.66 5 A 1 ATOM 38 O OG1 . THR A 1 5 ? -3.637 -4.829 -3.067 1.00 90.03 5 A 1 ATOM 39 C CG2 . THR A 1 5 ? -5.246 -3.075 -3.296 1.00 87.86 5 A 1 ATOM 40 N N . ARG A 1 6 ? -3.919 -1.582 -0.569 1.00 96.45 6 A 1 ATOM 41 C CA . ARG A 1 6 ? -3.038 -0.419 -0.485 1.00 96.73 6 A 1 ATOM 42 C C . ARG A 1 6 ? -2.540 -0.196 0.935 1.00 97.35 6 A 1 ATOM 43 O O . ARG A 1 6 ? -1.412 0.251 1.133 1.00 96.07 6 A 1 ATOM 44 C CB . ARG A 1 6 ? -3.776 0.829 -0.977 1.00 95.88 6 A 1 ATOM 45 C CG . ARG A 1 6 ? -3.360 1.226 -2.380 1.00 91.27 6 A 1 ATOM 46 C CD . ARG A 1 6 ? -2.092 2.056 -2.350 1.00 87.75 6 A 1 ATOM 47 N NE . ARG A 1 6 ? -1.188 1.674 -3.437 1.00 83.88 6 A 1 ATOM 48 C CZ . ARG A 1 6 ? -0.036 2.279 -3.685 1.00 81.61 6 A 1 ATOM 49 N NH1 . ARG A 1 6 ? 0.369 3.288 -2.943 1.00 75.89 6 A 1 ATOM 50 N NH2 . ARG A 1 6 ? 0.728 1.866 -4.688 1.00 76.02 6 A 1 ATOM 51 N N . LEU A 1 7 ? -3.374 -0.509 1.904 1.00 96.77 7 A 1 ATOM 52 C CA . LEU A 1 7 ? -3.021 -0.322 3.307 1.00 96.88 7 A 1 ATOM 53 C C . LEU A 1 7 ? -1.880 -1.246 3.731 1.00 97.21 7 A 1 ATOM 54 O O . LEU A 1 7 ? -1.020 -0.853 4.522 1.00 96.29 7 A 1 ATOM 55 C CB . LEU A 1 7 ? -4.251 -0.573 4.182 1.00 96.78 7 A 1 ATOM 56 C CG . LEU A 1 7 ? -5.299 0.540 4.138 1.00 94.53 7 A 1 ATOM 57 C CD1 . LEU A 1 7 ? -6.647 0.036 4.624 1.00 91.30 7 A 1 ATOM 58 C CD2 . LEU A 1 7 ? -4.849 1.721 4.992 1.00 90.49 7 A 1 ATOM 59 N N . LEU A 1 8 ? -1.884 -2.453 3.208 1.00 97.13 8 A 1 ATOM 60 C CA . LEU A 1 8 ? -0.849 -3.434 3.542 1.00 97.06 8 A 1 ATOM 61 C C . LEU A 1 8 ? 0.524 -3.043 2.981 1.00 97.34 8 A 1 ATOM 62 O O . LEU A 1 8 ? 1.488 -2.917 3.742 1.00 96.81 8 A 1 ATOM 63 C CB . LEU A 1 8 ? -1.272 -4.824 3.052 1.00 96.69 8 A 1 ATOM 64 C CG . LEU A 1 8 ? -0.373 -5.965 3.505 1.00 92.60 8 A 1 ATOM 65 C CD1 . LEU A 1 8 ? -0.590 -6.278 4.979 1.00 89.06 8 A 1 ATOM 66 C CD2 . LEU A 1 8 ? -0.638 -7.202 2.663 1.00 88.50 8 A 1 ATOM 67 N N . PRO A 1 9 ? 0.643 -2.859 1.654 1.00 97.22 9 A 1 ATOM 68 C CA . PRO A 1 9 ? 1.928 -2.502 1.044 1.00 97.23 9 A 1 ATOM 69 C C . PRO A 1 9 ? 2.355 -1.073 1.343 1.00 97.64 9 A 1 ATOM 70 O O . PRO A 1 9 ? 3.548 -0.791 1.457 1.00 97.07 9 A 1 ATOM 71 C CB . PRO A 1 9 ? 1.673 -2.691 -0.456 1.00 96.36 9 A 1 ATOM 72 C CG . PRO A 1 9 ? 0.212 -2.503 -0.621 1.00 95.30 9 A 1 ATOM 73 C CD . PRO A 1 9 ? -0.426 -2.989 0.654 1.00 96.51 9 A 1 ATOM 74 N N . LEU A 1 10 ? 1.405 -0.183 1.485 1.00 96.45 10 A 1 ATOM 75 C CA . LEU A 1 10 ? 1.692 1.216 1.781 1.00 96.38 10 A 1 ATOM 76 C C . LEU A 1 10 ? 2.332 1.358 3.156 1.00 97.05 10 A 1 ATOM 77 O O . LEU A 1 10 ? 3.271 2.135 3.331 1.00 96.45 10 A 1 ATOM 78 C CB . LEU A 1 10 ? 0.406 2.033 1.712 1.00 95.75 10 A 1 ATOM 79 C CG . LEU A 1 10 ? 0.611 3.540 1.726 1.00 91.24 10 A 1 ATOM 80 C CD1 . LEU A 1 10 ? 1.177 4.021 0.396 1.00 88.92 10 A 1 ATOM 81 C CD2 . LEU A 1 10 ? -0.704 4.247 2.020 1.00 88.60 10 A 1 ATOM 82 N N . ALA A 1 11 ? 1.833 0.612 4.109 1.00 96.31 11 A 1 ATOM 83 C CA . ALA A 1 11 ? 2.356 0.649 5.471 1.00 96.32 11 A 1 ATOM 84 C C . ALA A 1 11 ? 3.805 0.179 5.515 1.00 96.91 11 A 1 ATOM 85 O O . ALA A 1 11 ? 4.629 0.752 6.226 1.00 96.20 11 A 1 ATOM 86 C CB . ALA A 1 11 ? 1.499 -0.225 6.380 1.00 95.61 11 A 1 ATOM 87 N N . ALA A 1 12 ? 4.111 -0.858 4.758 1.00 97.18 12 A 1 ATOM 88 C CA . ALA A 1 12 ? 5.462 -1.410 4.711 1.00 97.16 12 A 1 ATOM 89 C C . ALA A 1 12 ? 6.425 -0.469 3.988 1.00 97.56 12 A 1 ATOM 90 O O . ALA A 1 12 ? 7.579 -0.325 4.389 1.00 96.43 12 A 1 ATOM 91 C CB . ALA A 1 12 ? 5.441 -2.771 4.025 1.00 96.48 12 A 1 ATOM 92 N N . LEU A 1 13 ? 5.948 0.167 2.928 1.00 97.15 13 A 1 ATOM 93 C CA . LEU A 1 13 ? 6.761 1.094 2.147 1.00 96.92 13 A 1 ATOM 94 C C . LEU A 1 13 ? 7.062 2.363 2.933 1.00 97.39 13 A 1 ATOM 95 O O . LEU A 1 13 ? 8.208 2.816 2.976 1.00 96.69 13 A 1 ATOM 96 C CB . LEU A 1 13 ? 6.045 1.435 0.843 1.00 96.51 13 A 1 ATOM 97 C CG . LEU A 1 13 ? 6.866 2.251 -0.146 1.00 92.40 13 A 1 ATOM 98 C CD1 . LEU A 1 13 ? 7.972 1.407 -0.762 1.00 90.32 13 A 1 ATOM 99 C CD2 . LEU A 1 13 ? 5.977 2.827 -1.228 1.00 89.88 13 A 1 ATOM 100 N N . VAL A 1 14 ? 6.059 2.925 3.546 1.00 96.94 14 A 1 ATOM 101 C CA . VAL A 1 14 ? 6.205 4.146 4.336 1.00 96.85 14 A 1 ATOM 102 C C . VAL A 1 14 ? 7.073 3.897 5.566 1.00 97.09 14 A 1 ATOM 103 O O . VAL A 1 14 ? 7.854 4.760 5.971 1.00 96.27 14 A 1 ATOM 104 C CB . VAL A 1 14 ? 4.827 4.689 4.758 1.00 96.07 14 A 1 ATOM 105 C CG1 . VAL A 1 14 ? 4.978 5.886 5.684 1.00 92.39 14 A 1 ATOM 106 C CG2 . VAL A 1 14 ? 4.009 5.076 3.541 1.00 92.38 14 A 1 ATOM 107 N N . LEU A 1 15 ? 6.948 2.729 6.143 1.00 96.88 15 A 1 ATOM 108 C CA . LEU A 1 15 ? 7.722 2.368 7.329 1.00 96.42 15 A 1 ATOM 109 C C . LEU A 1 15 ? 9.206 2.228 6.995 1.00 96.72 15 A 1 ATOM 110 O O . LEU A 1 15 ? 10.070 2.562 7.810 1.00 95.63 15 A 1 ATOM 111 C CB . LEU A 1 15 ? 7.190 1.056 7.916 1.00 95.62 15 A 1 ATOM 112 C CG . LEU A 1 15 ? 7.331 0.939 9.432 1.00 92.40 15 A 1 ATOM 113 C CD1 . LEU A 1 15 ? 6.212 1.687 10.138 1.00 89.34 15 A 1 ATOM 114 C CD2 . LEU A 1 15 ? 7.338 -0.518 9.856 1.00 88.40 15 A 1 ATOM 115 N N . SER A 1 16 ? 9.499 1.727 5.801 1.00 96.67 16 A 1 ATOM 116 C CA . SER A 1 16 ? 10.874 1.530 5.346 1.00 96.57 16 A 1 ATOM 117 C C . SER A 1 16 ? 11.492 2.819 4.808 1.00 96.70 16 A 1 ATOM 118 O O . SER A 1 16 ? 12.715 2.954 4.748 1.00 94.91 16 A 1 ATOM 119 C CB . SER A 1 16 ? 10.914 0.448 4.269 1.00 95.25 16 A 1 ATOM 120 O OG . SER A 1 16 ? 12.224 -0.020 4.076 1.00 86.94 16 A 1 ATOM 121 N N . ALA A 1 17 ? 10.653 3.759 4.414 1.00 94.95 17 A 1 ATOM 122 C CA . ALA A 1 17 ? 11.111 5.019 3.843 1.00 93.13 17 A 1 ATOM 123 C C . ALA A 1 17 ? 10.498 6.214 4.567 1.00 91.66 17 A 1 ATOM 124 O O . ALA A 1 17 ? 9.269 6.267 4.704 1.00 88.20 17 A 1 ATOM 125 C CB . ALA A 1 17 ? 10.782 5.073 2.362 1.00 90.19 17 A 1 ATOM 126 O OXT . ALA A 1 17 ? 11.232 7.126 4.956 1.00 81.57 17 A 1 #