# 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_spkb17504 # _entry.id spkb17504 # 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 LEU y LEUCINE CC(C)C[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" # _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 LEU 1 1 n LEU 2 1 n LEU 3 1 n ALA 4 1 n GLY 5 1 n LEU 6 1 n CYS 7 1 n CYS 8 1 n LEU 9 1 n LEU 10 1 n PRO 11 1 n GLY 12 1 n SER 13 1 n LEU 14 1 n ALA 15 # _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 @ 2025-07-08 19:50:30)" _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 91.60 _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 LEU 1 2 87.73 1 1 A LEU 2 2 92.91 1 2 A LEU 3 2 93.14 1 3 A ALA 4 2 95.58 1 4 A GLY 5 2 95.72 1 5 A LEU 6 2 92.70 1 6 A CYS 7 2 93.60 1 7 A CYS 8 2 93.86 1 8 A LEU 9 2 94.69 1 9 A LEU 10 2 93.16 1 10 A PRO 11 2 93.63 1 11 A GLY 12 2 92.01 1 12 A SER 13 2 90.10 1 13 A LEU 14 2 85.39 1 14 A ALA 15 2 82.15 1 15 # _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 LEU . 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 GLY . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n CYS . 7 A 7 A 8 1 n CYS . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n PRO . 11 A 11 A 12 1 n GLY . 12 A 12 A 13 1 n SER . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n ALA . 15 A 15 # _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 . LEU A 1 1 ? 8.672 0.350 3.826 1.00 89.07 1 A 1 ATOM 2 C CA . LEU A 1 1 ? 8.213 -1.051 4.039 1.00 91.56 1 A 1 ATOM 3 C C . LEU A 1 1 ? 7.041 -1.373 3.100 1.00 93.27 1 A 1 ATOM 4 O O . LEU A 1 1 ? 6.336 -0.480 2.658 1.00 91.33 1 A 1 ATOM 5 C CB . LEU A 1 1 ? 7.765 -1.196 5.497 1.00 87.97 1 A 1 ATOM 6 C CG . LEU A 1 1 ? 8.956 -1.017 6.458 1.00 85.40 1 A 1 ATOM 7 C CD1 . LEU A 1 1 ? 8.443 -0.835 7.881 1.00 82.81 1 A 1 ATOM 8 C CD2 . LEU A 1 1 ? 9.873 -2.252 6.394 1.00 80.45 1 A 1 ATOM 9 N N . LEU A 1 2 ? 6.825 -2.636 2.800 1.00 92.97 2 A 1 ATOM 10 C CA . LEU A 1 2 ? 5.736 -3.063 1.899 1.00 94.53 2 A 1 ATOM 11 C C . LEU A 1 2 ? 4.368 -2.841 2.555 1.00 96.29 2 A 1 ATOM 12 O O . LEU A 1 2 ? 3.443 -2.332 1.928 1.00 96.16 2 A 1 ATOM 13 C CB . LEU A 1 2 ? 5.930 -4.553 1.569 1.00 93.82 2 A 1 ATOM 14 C CG . LEU A 1 2 ? 6.738 -4.765 0.286 1.00 91.86 2 A 1 ATOM 15 C CD1 . LEU A 1 2 ? 5.981 -4.203 -0.907 1.00 89.71 2 A 1 ATOM 16 C CD2 . LEU A 1 2 ? 8.109 -4.121 0.385 1.00 87.95 2 A 1 ATOM 17 N N . LEU A 1 3 ? 4.238 -3.233 3.808 1.00 93.74 3 A 1 ATOM 18 C CA . LEU A 1 3 ? 2.954 -3.082 4.530 1.00 94.92 3 A 1 ATOM 19 C C . LEU A 1 3 ? 2.495 -1.623 4.531 1.00 96.16 3 A 1 ATOM 20 O O . LEU A 1 3 ? 1.302 -1.343 4.506 1.00 96.05 3 A 1 ATOM 21 C CB . LEU A 1 3 ? 3.157 -3.579 5.972 1.00 94.04 3 A 1 ATOM 22 C CG . LEU A 1 3 ? 3.190 -5.111 6.026 1.00 91.69 3 A 1 ATOM 23 C CD1 . LEU A 1 3 ? 3.813 -5.565 7.350 1.00 89.82 3 A 1 ATOM 24 C CD2 . LEU A 1 3 ? 1.771 -5.667 5.920 1.00 88.66 3 A 1 ATOM 25 N N . ALA A 1 4 ? 3.423 -0.697 4.538 1.00 95.75 4 A 1 ATOM 26 C CA . ALA A 1 4 ? 3.068 0.737 4.548 1.00 95.82 4 A 1 ATOM 27 C C . ALA A 1 4 ? 2.325 1.118 3.263 1.00 96.36 4 A 1 ATOM 28 O O . ALA A 1 4 ? 1.580 2.089 3.232 1.00 95.25 4 A 1 ATOM 29 C CB . ALA A 1 4 ? 4.351 1.558 4.685 1.00 94.74 4 A 1 ATOM 30 N N . GLY A 1 5 ? 2.524 0.373 2.197 1.00 95.67 5 A 1 ATOM 31 C CA . GLY A 1 5 ? 1.866 0.671 0.913 1.00 95.69 5 A 1 ATOM 32 C C . GLY A 1 5 ? 0.435 0.148 0.855 1.00 96.27 5 A 1 ATOM 33 O O . GLY A 1 5 ? -0.367 0.619 0.056 1.00 95.26 5 A 1 ATOM 34 N N . LEU A 1 6 ? 0.112 -0.831 1.667 1.00 94.38 6 A 1 ATOM 35 C CA . LEU A 1 6 ? -1.248 -1.406 1.687 1.00 94.60 6 A 1 ATOM 36 C C . LEU A 1 6 ? -1.887 -1.274 3.071 1.00 95.45 6 A 1 ATOM 37 O O . LEU A 1 6 ? -2.822 -1.996 3.399 1.00 94.60 6 A 1 ATOM 38 C CB . LEU A 1 6 ? -1.148 -2.879 1.268 1.00 93.85 6 A 1 ATOM 39 C CG . LEU A 1 6 ? -0.141 -3.638 2.139 1.00 91.15 6 A 1 ATOM 40 C CD1 . LEU A 1 6 ? -0.884 -4.456 3.201 1.00 89.49 6 A 1 ATOM 41 C CD2 . LEU A 1 6 ? 0.697 -4.560 1.263 1.00 88.10 6 A 1 ATOM 42 N N . CYS A 1 7 ? -1.389 -0.363 3.871 1.00 94.73 7 A 1 ATOM 43 C CA . CYS A 1 7 ? -1.933 -0.174 5.230 1.00 94.80 7 A 1 ATOM 44 C C . CYS A 1 7 ? -3.115 0.797 5.207 1.00 94.97 7 A 1 ATOM 45 O O . CYS A 1 7 ? -4.249 0.430 5.489 1.00 93.35 7 A 1 ATOM 46 C CB . CYS A 1 7 ? -0.825 0.377 6.131 1.00 93.45 7 A 1 ATOM 47 S SG . CYS A 1 7 ? -1.516 0.985 7.693 1.00 90.31 7 A 1 ATOM 48 N N . CYS A 1 8 ? -2.851 2.043 4.868 1.00 94.33 8 A 1 ATOM 49 C CA . CYS A 1 8 ? -3.908 3.070 4.875 1.00 94.77 8 A 1 ATOM 50 C C . CYS A 1 8 ? -3.760 4.019 3.687 1.00 95.30 8 A 1 ATOM 51 O O . CYS A 1 8 ? -4.658 4.796 3.402 1.00 93.61 8 A 1 ATOM 52 C CB . CYS A 1 8 ? -3.775 3.859 6.182 1.00 93.54 8 A 1 ATOM 53 S SG . CYS A 1 8 ? -3.565 2.748 7.611 1.00 91.63 8 A 1 ATOM 54 N N . LEU A 1 9 ? -2.645 3.971 2.988 1.00 95.30 9 A 1 ATOM 55 C CA . LEU A 1 9 ? -2.403 4.864 1.843 1.00 95.77 9 A 1 ATOM 56 C C . LEU A 1 9 ? -3.118 4.357 0.585 1.00 96.59 9 A 1 ATOM 57 O O . LEU A 1 9 ? -2.593 4.462 -0.516 1.00 95.80 9 A 1 ATOM 58 C CB . LEU A 1 9 ? -0.894 4.963 1.603 1.00 95.41 9 A 1 ATOM 59 C CG . LEU A 1 9 ? -0.549 6.226 0.816 1.00 94.33 9 A 1 ATOM 60 C CD1 . LEU A 1 9 ? -0.683 7.446 1.714 1.00 92.69 9 A 1 ATOM 61 C CD2 . LEU A 1 9 ? 0.879 6.135 0.284 1.00 91.64 9 A 1 ATOM 62 N N . LEU A 1 10 ? -4.319 3.826 0.733 1.00 95.58 10 A 1 ATOM 63 C CA . LEU A 1 10 ? -5.110 3.317 -0.408 1.00 95.19 10 A 1 ATOM 64 C C . LEU A 1 10 ? -4.288 2.359 -1.273 1.00 95.72 10 A 1 ATOM 65 O O . LEU A 1 10 ? -3.302 2.756 -1.869 1.00 95.05 10 A 1 ATOM 66 C CB . LEU A 1 10 ? -5.579 4.510 -1.250 1.00 94.38 10 A 1 ATOM 67 C CG . LEU A 1 10 ? -6.761 4.131 -2.137 1.00 92.24 10 A 1 ATOM 68 C CD1 . LEU A 1 10 ? -8.044 4.122 -1.311 1.00 89.44 10 A 1 ATOM 69 C CD2 . LEU A 1 10 ? -6.900 5.158 -3.265 1.00 87.68 10 A 1 ATOM 70 N N . PRO A 1 11 ? -4.698 1.094 -1.387 1.00 95.23 11 A 1 ATOM 71 C CA . PRO A 1 11 ? -3.949 0.106 -2.182 1.00 94.81 11 A 1 ATOM 72 C C . PRO A 1 11 ? -4.073 0.388 -3.686 1.00 94.82 11 A 1 ATOM 73 O O . PRO A 1 11 ? -5.058 0.952 -4.147 1.00 92.81 11 A 1 ATOM 74 C CB . PRO A 1 11 ? -4.629 -1.221 -1.817 1.00 93.18 11 A 1 ATOM 75 C CG . PRO A 1 11 ? -6.016 -0.824 -1.395 1.00 91.05 11 A 1 ATOM 76 C CD . PRO A 1 11 ? -5.886 0.552 -0.755 1.00 93.49 11 A 1 ATOM 77 N N . GLY A 1 12 ? -3.076 -0.030 -4.451 1.00 92.36 12 A 1 ATOM 78 C CA . GLY A 1 12 ? -3.098 0.192 -5.908 1.00 91.66 12 A 1 ATOM 79 C C . GLY A 1 12 ? -4.120 -0.697 -6.602 1.00 93.00 12 A 1 ATOM 80 O O . GLY A 1 12 ? -4.636 -0.352 -7.659 1.00 91.02 12 A 1 ATOM 81 N N . SER A 1 13 ? -4.427 -1.853 -6.033 1.00 91.72 13 A 1 ATOM 82 C CA . SER A 1 13 ? -5.412 -2.781 -6.623 1.00 92.17 13 A 1 ATOM 83 C C . SER A 1 13 ? -6.811 -2.174 -6.592 1.00 92.55 13 A 1 ATOM 84 O O . SER A 1 13 ? -7.501 -2.121 -7.604 1.00 90.08 13 A 1 ATOM 85 C CB . SER A 1 13 ? -5.409 -4.091 -5.839 1.00 90.70 13 A 1 ATOM 86 O OG . SER A 1 13 ? -6.324 -4.982 -6.443 1.00 83.38 13 A 1 ATOM 87 N N . LEU A 1 14 ? -7.251 -1.715 -5.439 1.00 89.91 14 A 1 ATOM 88 C CA . LEU A 1 14 ? -8.585 -1.102 -5.299 1.00 89.01 14 A 1 ATOM 89 C C . LEU A 1 14 ? -8.627 0.237 -6.027 1.00 90.22 14 A 1 ATOM 90 O O . LEU A 1 14 ? -9.611 0.554 -6.693 1.00 86.47 14 A 1 ATOM 91 C CB . LEU A 1 14 ? -8.887 -0.921 -3.805 1.00 86.56 14 A 1 ATOM 92 C CG . LEU A 1 14 ? -10.375 -0.723 -3.560 1.00 84.31 14 A 1 ATOM 93 C CD1 . LEU A 1 14 ? -10.792 -1.436 -2.285 1.00 79.76 14 A 1 ATOM 94 C CD2 . LEU A 1 14 ? -10.690 0.768 -3.442 1.00 76.84 14 A 1 ATOM 95 N N . ALA A 1 15 ? -7.554 1.013 -5.931 1.00 87.82 15 A 1 ATOM 96 C CA . ALA A 1 15 ? -7.467 2.328 -6.596 1.00 85.97 15 A 1 ATOM 97 C C . ALA A 1 15 ? -8.734 3.147 -6.328 1.00 84.29 15 A 1 ATOM 98 O O . ALA A 1 15 ? -9.482 3.437 -7.262 1.00 79.83 15 A 1 ATOM 99 C CB . ALA A 1 15 ? -7.275 2.118 -8.090 1.00 81.05 15 A 1 ATOM 100 O OXT . ALA A 1 15 ? -8.933 3.517 -5.144 1.00 73.97 15 A 1 #