# 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_spkb39408 # _entry.id spkb39408 # 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 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" "C6 H15 N2 O2" 147.195 LYS y LYSINE C(CC[NH3+])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" "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 LYS 2 1 n THR 3 1 n ALA 4 1 n LEU 5 1 n VAL 6 1 n LEU 7 1 n ILE 8 1 n LEU 9 1 n ALA 10 1 n THR 11 1 n ALA 12 1 n THR 13 1 n LEU 14 1 n ALA 15 1 n VAL 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 @ 2025-07-06 16:08:46)" _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 96.35 _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 89.68 1 1 A LYS 2 2 92.84 1 2 A THR 3 2 96.63 1 3 A ALA 4 2 98.44 1 4 A LEU 5 2 97.00 1 5 A VAL 6 2 98.22 1 6 A LEU 7 2 96.84 1 7 A ILE 8 2 98.06 1 8 A LEU 9 2 96.78 1 9 A ALA 10 2 98.59 1 10 A THR 11 2 97.57 1 11 A ALA 12 2 98.59 1 12 A THR 13 2 97.32 1 13 A LEU 14 2 96.45 1 14 A ALA 15 2 98.31 1 15 A VAL 16 2 96.49 1 16 A ALA 17 2 93.59 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 LYS . 2 A 2 A 3 1 n THR . 3 A 3 A 4 1 n ALA . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n VAL . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n ILE . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n THR . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n THR . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n VAL . 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 ? -7.785 5.215 11.776 1.00 94.89 1 A 1 ATOM 2 C CA . MET A 1 1 ? -7.740 3.820 11.302 1.00 94.89 1 A 1 ATOM 3 C C . MET A 1 1 ? -6.391 3.511 10.654 1.00 95.57 1 A 1 ATOM 4 O O . MET A 1 1 ? -5.767 4.387 10.052 1.00 94.06 1 A 1 ATOM 5 C CB . MET A 1 1 ? -8.859 3.570 10.290 1.00 92.00 1 A 1 ATOM 6 C CG . MET A 1 1 ? -8.796 4.516 9.102 1.00 88.32 1 A 1 ATOM 7 S SD . MET A 1 1 ? -10.175 4.309 7.967 1.00 84.22 1 A 1 ATOM 8 C CE . MET A 1 1 ? -11.459 5.127 8.893 1.00 73.50 1 A 1 ATOM 9 N N . LYS A 1 2 ? -5.944 2.268 10.773 1.00 96.23 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -4.646 1.848 10.228 1.00 97.41 2 A 1 ATOM 11 C C . LYS A 1 2 ? -4.749 1.443 8.757 1.00 97.97 2 A 1 ATOM 12 O O . LYS A 1 2 ? -3.740 1.416 8.056 1.00 97.67 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -4.116 0.675 11.051 1.00 96.64 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -3.879 1.050 12.514 1.00 93.11 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -2.793 2.102 12.648 1.00 90.11 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -2.612 2.523 14.094 1.00 85.56 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -2.130 1.401 14.921 1.00 80.85 2 A 1 ATOM 18 N N . THR A 1 3 ? -5.940 1.113 8.288 1.00 97.38 3 A 1 ATOM 19 C CA . THR A 1 3 ? -6.144 0.703 6.892 1.00 97.70 3 A 1 ATOM 20 C C . THR A 1 3 ? -5.628 1.769 5.925 1.00 98.02 3 A 1 ATOM 21 O O . THR A 1 3 ? -5.001 1.453 4.914 1.00 97.74 3 A 1 ATOM 22 C CB . THR A 1 3 ? -7.630 0.458 6.615 1.00 97.23 3 A 1 ATOM 23 O OG1 . THR A 1 3 ? -8.137 -0.484 7.562 1.00 94.49 3 A 1 ATOM 24 C CG2 . THR A 1 3 ? -7.816 -0.088 5.208 1.00 93.83 3 A 1 ATOM 25 N N . ALA A 1 4 ? -5.889 3.026 6.225 1.00 98.23 4 A 1 ATOM 26 C CA . ALA A 1 4 ? -5.439 4.125 5.370 1.00 98.49 4 A 1 ATOM 27 C C . ALA A 1 4 ? -3.914 4.134 5.258 1.00 98.66 4 A 1 ATOM 28 O O . ALA A 1 4 ? -3.360 4.345 4.179 1.00 98.51 4 A 1 ATOM 29 C CB . ALA A 1 4 ? -5.934 5.451 5.934 1.00 98.32 4 A 1 ATOM 30 N N . LEU A 1 5 ? -3.233 3.886 6.363 1.00 98.43 5 A 1 ATOM 31 C CA . LEU A 1 5 ? -1.770 3.867 6.377 1.00 98.53 5 A 1 ATOM 32 C C . LEU A 1 5 ? -1.240 2.722 5.521 1.00 98.66 5 A 1 ATOM 33 O O . LEU A 1 5 ? -0.233 2.872 4.830 1.00 98.62 5 A 1 ATOM 34 C CB . LEU A 1 5 ? -1.273 3.715 7.814 1.00 98.42 5 A 1 ATOM 35 C CG . LEU A 1 5 ? -1.610 4.914 8.702 1.00 95.43 5 A 1 ATOM 36 C CD1 . LEU A 1 5 ? -1.217 4.614 10.138 1.00 93.53 5 A 1 ATOM 37 C CD2 . LEU A 1 5 ? -0.881 6.158 8.210 1.00 94.34 5 A 1 ATOM 38 N N . VAL A 1 6 ? -1.914 1.586 5.567 1.00 98.58 6 A 1 ATOM 39 C CA . VAL A 1 6 ? -1.505 0.420 4.781 1.00 98.59 6 A 1 ATOM 40 C C . VAL A 1 6 ? -1.598 0.725 3.288 1.00 98.66 6 A 1 ATOM 41 O O . VAL A 1 6 ? -0.704 0.376 2.513 1.00 98.60 6 A 1 ATOM 42 C CB . VAL A 1 6 ? -2.383 -0.795 5.118 1.00 98.39 6 A 1 ATOM 43 C CG1 . VAL A 1 6 ? -2.021 -1.979 4.230 1.00 97.53 6 A 1 ATOM 44 C CG2 . VAL A 1 6 ? -2.193 -1.169 6.581 1.00 97.20 6 A 1 ATOM 45 N N . LEU A 1 7 ? -2.678 1.375 2.881 1.00 98.60 7 A 1 ATOM 46 C CA . LEU A 1 7 ? -2.876 1.714 1.471 1.00 98.55 7 A 1 ATOM 47 C C . LEU A 1 7 ? -1.784 2.668 0.994 1.00 98.68 7 A 1 ATOM 48 O O . LEU A 1 7 ? -1.236 2.509 -0.098 1.00 98.66 7 A 1 ATOM 49 C CB . LEU A 1 7 ? -4.250 2.364 1.283 1.00 98.37 7 A 1 ATOM 50 C CG . LEU A 1 7 ? -5.414 1.401 1.524 1.00 94.33 7 A 1 ATOM 51 C CD1 . LEU A 1 7 ? -6.729 2.169 1.530 1.00 93.35 7 A 1 ATOM 52 C CD2 . LEU A 1 7 ? -5.445 0.326 0.448 1.00 94.22 7 A 1 ATOM 53 N N . ILE A 1 8 ? -1.472 3.650 1.799 1.00 98.58 8 A 1 ATOM 54 C CA . ILE A 1 8 ? -0.438 4.626 1.458 1.00 98.58 8 A 1 ATOM 55 C C . ILE A 1 8 ? 0.921 3.937 1.367 1.00 98.65 8 A 1 ATOM 56 O O . ILE A 1 8 ? 1.707 4.208 0.453 1.00 98.57 8 A 1 ATOM 57 C CB . ILE A 1 8 ? -0.396 5.751 2.508 1.00 98.57 8 A 1 ATOM 58 C CG1 . ILE A 1 8 ? -1.717 6.537 2.481 1.00 98.02 8 A 1 ATOM 59 C CG2 . ILE A 1 8 ? 0.780 6.693 2.228 1.00 97.64 8 A 1 ATOM 60 C CD1 . ILE A 1 8 ? -1.866 7.475 3.661 1.00 95.88 8 A 1 ATOM 61 N N . LEU A 1 9 ? 1.192 3.050 2.300 1.00 98.61 9 A 1 ATOM 62 C CA . LEU A 1 9 ? 2.465 2.333 2.322 1.00 98.54 9 A 1 ATOM 63 C C . LEU A 1 9 ? 2.612 1.451 1.088 1.00 98.65 9 A 1 ATOM 64 O O . LEU A 1 9 ? 3.684 1.392 0.486 1.00 98.57 9 A 1 ATOM 65 C CB . LEU A 1 9 ? 2.543 1.473 3.585 1.00 98.30 9 A 1 ATOM 66 C CG . LEU A 1 9 ? 3.871 0.727 3.719 1.00 94.25 9 A 1 ATOM 67 C CD1 . LEU A 1 9 ? 5.021 1.712 3.857 1.00 93.31 9 A 1 ATOM 68 C CD2 . LEU A 1 9 ? 3.826 -0.192 4.931 1.00 93.97 9 A 1 ATOM 69 N N . ALA A 1 10 ? 1.540 0.768 0.705 1.00 98.65 10 A 1 ATOM 70 C CA . ALA A 1 10 ? 1.564 -0.104 -0.466 1.00 98.63 10 A 1 ATOM 71 C C . ALA A 1 10 ? 1.857 0.698 -1.729 1.00 98.74 10 A 1 ATOM 72 O O . ALA A 1 10 ? 2.667 0.291 -2.564 1.00 98.54 10 A 1 ATOM 73 C CB . ALA A 1 10 ? 0.224 -0.820 -0.598 1.00 98.40 10 A 1 ATOM 74 N N . THR A 1 11 ? 1.204 1.832 -1.872 1.00 98.65 11 A 1 ATOM 75 C CA . THR A 1 11 ? 1.399 2.686 -3.043 1.00 98.62 11 A 1 ATOM 76 C C . THR A 1 11 ? 2.831 3.211 -3.085 1.00 98.70 11 A 1 ATOM 77 O O . THR A 1 11 ? 3.471 3.218 -4.137 1.00 98.45 11 A 1 ATOM 78 C CB . THR A 1 11 ? 0.427 3.869 -3.009 1.00 98.35 11 A 1 ATOM 79 O OG1 . THR A 1 11 ? -0.911 3.381 -2.954 1.00 95.53 11 A 1 ATOM 80 C CG2 . THR A 1 11 ? 0.594 4.725 -4.258 1.00 94.72 11 A 1 ATOM 81 N N . ALA A 1 12 ? 3.335 3.639 -1.948 1.00 98.69 12 A 1 ATOM 82 C CA . ALA A 1 12 ? 4.694 4.166 -1.864 1.00 98.65 12 A 1 ATOM 83 C C . ALA A 1 12 ? 5.716 3.085 -2.200 1.00 98.73 12 A 1 ATOM 84 O O . ALA A 1 12 ? 6.709 3.350 -2.877 1.00 98.45 12 A 1 ATOM 85 C CB . ALA A 1 12 ? 4.946 4.708 -0.464 1.00 98.43 12 A 1 ATOM 86 N N . THR A 1 13 ? 5.474 1.868 -1.745 1.00 98.56 13 A 1 ATOM 87 C CA . THR A 1 13 ? 6.385 0.752 -2.003 1.00 98.50 13 A 1 ATOM 88 C C . THR A 1 13 ? 6.506 0.496 -3.500 1.00 98.60 13 A 1 ATOM 89 O O . THR A 1 13 ? 7.607 0.324 -4.023 1.00 98.30 13 A 1 ATOM 90 C CB . THR A 1 13 ? 5.882 -0.516 -1.314 1.00 98.14 13 A 1 ATOM 91 O OG1 . THR A 1 13 ? 5.791 -0.286 0.090 1.00 95.16 13 A 1 ATOM 92 C CG2 . THR A 1 13 ? 6.848 -1.664 -1.562 1.00 93.98 13 A 1 ATOM 93 N N . LEU A 1 14 ? 5.381 0.475 -4.207 1.00 98.68 14 A 1 ATOM 94 C CA . LEU A 1 14 ? 5.379 0.234 -5.647 1.00 98.57 14 A 1 ATOM 95 C C . LEU A 1 14 ? 6.084 1.361 -6.386 1.00 98.62 14 A 1 ATOM 96 O O . LEU A 1 14 ? 6.822 1.122 -7.341 1.00 98.20 14 A 1 ATOM 97 C CB . LEU A 1 14 ? 3.938 0.112 -6.143 1.00 98.20 14 A 1 ATOM 98 C CG . LEU A 1 14 ? 3.228 -1.138 -5.627 1.00 95.08 14 A 1 ATOM 99 C CD1 . LEU A 1 14 ? 1.756 -1.080 -5.983 1.00 92.33 14 A 1 ATOM 100 C CD2 . LEU A 1 14 ? 3.864 -2.388 -6.214 1.00 91.90 14 A 1 ATOM 101 N N . ALA A 1 15 ? 5.847 2.586 -5.968 1.00 98.46 15 A 1 ATOM 102 C CA . ALA A 1 15 ? 6.458 3.750 -6.605 1.00 98.40 15 A 1 ATOM 103 C C . ALA A 1 15 ? 7.962 3.803 -6.353 1.00 98.53 15 A 1 ATOM 104 O O . ALA A 1 15 ? 8.735 4.147 -7.249 1.00 98.15 15 A 1 ATOM 105 C CB . ALA A 1 15 ? 5.799 5.025 -6.087 1.00 98.01 15 A 1 ATOM 106 N N . VAL A 1 16 ? 8.382 3.471 -5.143 1.00 98.08 16 A 1 ATOM 107 C CA . VAL A 1 16 ? 9.799 3.500 -4.774 1.00 98.04 16 A 1 ATOM 108 C C . VAL A 1 16 ? 10.551 2.294 -5.321 1.00 98.25 16 A 1 ATOM 109 O O . VAL A 1 16 ? 11.729 2.395 -5.681 1.00 97.69 16 A 1 ATOM 110 C CB . VAL A 1 16 ? 9.950 3.560 -3.245 1.00 97.04 16 A 1 ATOM 111 C CG1 . VAL A 1 16 ? 11.419 3.503 -2.851 1.00 93.42 16 A 1 ATOM 112 C CG2 . VAL A 1 16 ? 9.324 4.837 -2.712 1.00 92.92 16 A 1 ATOM 113 N N . ALA A 1 17 ? 9.887 1.141 -5.381 1.00 97.07 17 A 1 ATOM 114 C CA . ALA A 1 17 ? 10.516 -0.086 -5.846 1.00 96.05 17 A 1 ATOM 115 C C . ALA A 1 17 ? 11.074 0.058 -7.261 1.00 95.12 17 A 1 ATOM 116 O O . ALA A 1 17 ? 10.515 0.833 -8.059 1.00 92.04 17 A 1 ATOM 117 C CB . ALA A 1 17 ? 9.519 -1.241 -5.778 1.00 94.07 17 A 1 ATOM 118 O OXT . ALA A 1 17 ? 12.068 -0.620 -7.577 1.00 87.18 17 A 1 #