# 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_spkb23808 # _entry.id spkb23808 # 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" "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" "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 ARG 2 1 n VAL 3 1 n ALA 4 1 n ALA 5 1 n SER 6 1 n THR 7 1 n VAL 8 1 n LEU 9 1 n LEU 10 1 n GLY 11 1 n VAL 12 1 n ALA 13 1 n SER 14 1 n ALA 15 1 n ALA 16 1 n SER 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 07:17:18)" _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 93.08 _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 85.95 1 1 A ARG 2 2 83.77 1 2 A VAL 3 2 94.48 1 3 A ALA 4 2 95.37 1 4 A ALA 5 2 96.25 1 5 A SER 6 2 94.23 1 6 A THR 7 2 95.39 1 7 A VAL 8 2 96.80 1 8 A LEU 9 2 95.86 1 9 A LEU 10 2 95.44 1 10 A GLY 11 2 96.76 1 11 A VAL 12 2 96.09 1 12 A ALA 13 2 96.96 1 13 A SER 14 2 95.17 1 14 A ALA 15 2 96.19 1 15 A ALA 16 2 94.83 1 16 A SER 17 2 84.46 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 VAL . 3 A 3 A 4 1 n ALA . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n SER . 6 A 6 A 7 1 n THR . 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 GLY . 11 A 11 A 12 1 n VAL . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n SER . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n ALA . 16 A 16 A 17 1 n SER . 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 ? -1.519 1.934 13.953 1.00 90.19 1 A 1 ATOM 2 C CA . MET A 1 1 ? -1.371 3.164 13.166 1.00 91.55 1 A 1 ATOM 3 C C . MET A 1 1 ? -0.568 2.903 11.889 1.00 92.60 1 A 1 ATOM 4 O O . MET A 1 1 ? 0.261 3.706 11.478 1.00 89.60 1 A 1 ATOM 5 C CB . MET A 1 1 ? -0.677 4.240 14.002 1.00 88.20 1 A 1 ATOM 6 C CG . MET A 1 1 ? -1.467 4.602 15.249 1.00 84.57 1 A 1 ATOM 7 S SD . MET A 1 1 ? -0.618 5.811 16.277 1.00 81.37 1 A 1 ATOM 8 C CE . MET A 1 1 ? -1.795 5.982 17.610 1.00 69.55 1 A 1 ATOM 9 N N . ARG A 1 2 ? -0.821 1.762 11.268 1.00 88.49 2 A 1 ATOM 10 C CA . ARG A 1 2 ? -0.129 1.375 10.040 1.00 93.44 2 A 1 ATOM 11 C C . ARG A 1 2 ? -1.110 1.317 8.877 1.00 95.31 2 A 1 ATOM 12 O O . ARG A 1 2 ? -0.841 0.693 7.852 1.00 93.39 2 A 1 ATOM 13 C CB . ARG A 1 2 ? 0.550 0.011 10.216 1.00 90.67 2 A 1 ATOM 14 C CG . ARG A 1 2 ? 1.415 -0.071 11.462 1.00 84.45 2 A 1 ATOM 15 C CD . ARG A 1 2 ? 1.927 -1.479 11.664 1.00 84.80 2 A 1 ATOM 16 N NE . ARG A 1 2 ? 2.253 -1.737 13.071 1.00 78.00 2 A 1 ATOM 17 C CZ . ARG A 1 2 ? 2.498 -2.946 13.567 1.00 76.46 2 A 1 ATOM 18 N NH1 . ARG A 1 2 ? 2.488 -4.011 12.784 1.00 68.34 2 A 1 ATOM 19 N NH2 . ARG A 1 2 ? 2.740 -3.086 14.857 1.00 68.07 2 A 1 ATOM 20 N N . VAL A 1 3 ? -2.254 1.949 9.038 1.00 95.13 3 A 1 ATOM 21 C CA . VAL A 1 3 ? -3.299 1.956 8.021 1.00 96.23 3 A 1 ATOM 22 C C . VAL A 1 3 ? -2.816 2.645 6.753 1.00 97.31 3 A 1 ATOM 23 O O . VAL A 1 3 ? -3.135 2.216 5.640 1.00 96.70 3 A 1 ATOM 24 C CB . VAL A 1 3 ? -4.571 2.646 8.543 1.00 94.48 3 A 1 ATOM 25 C CG1 . VAL A 1 3 ? -5.666 2.622 7.489 1.00 90.62 3 A 1 ATOM 26 C CG2 . VAL A 1 3 ? -5.051 1.981 9.823 1.00 90.87 3 A 1 ATOM 27 N N . ALA A 1 4 ? -2.035 3.701 6.931 1.00 94.43 4 A 1 ATOM 28 C CA . ALA A 1 4 ? -1.501 4.451 5.798 1.00 95.65 4 A 1 ATOM 29 C C . ALA A 1 4 ? -0.642 3.563 4.904 1.00 96.70 4 A 1 ATOM 30 O O . ALA A 1 4 ? -0.805 3.545 3.685 1.00 95.95 4 A 1 ATOM 31 C CB . ALA A 1 4 ? -0.692 5.643 6.294 1.00 94.10 4 A 1 ATOM 32 N N . ALA A 1 5 ? 0.268 2.817 5.518 1.00 95.64 5 A 1 ATOM 33 C CA . ALA A 1 5 ? 1.155 1.929 4.772 1.00 96.49 5 A 1 ATOM 34 C C . ALA A 1 5 ? 0.377 0.819 4.071 1.00 97.24 5 A 1 ATOM 35 O O . ALA A 1 5 ? 0.608 0.528 2.896 1.00 96.49 5 A 1 ATOM 36 C CB . ALA A 1 5 ? 2.200 1.333 5.706 1.00 95.40 5 A 1 ATOM 37 N N . SER A 1 6 ? -0.556 0.205 4.790 1.00 96.03 6 A 1 ATOM 38 C CA . SER A 1 6 ? -1.357 -0.886 4.246 1.00 96.26 6 A 1 ATOM 39 C C . SER A 1 6 ? -2.254 -0.414 3.109 1.00 97.11 6 A 1 ATOM 40 O O . SER A 1 6 ? -2.314 -1.041 2.051 1.00 96.35 6 A 1 ATOM 41 C CB . SER A 1 6 ? -2.208 -1.514 5.345 1.00 94.90 6 A 1 ATOM 42 O OG . SER A 1 6 ? -1.385 -2.053 6.363 1.00 84.70 6 A 1 ATOM 43 N N . THR A 1 7 ? -2.941 0.699 3.321 1.00 96.38 7 A 1 ATOM 44 C CA . THR A 1 7 ? -3.852 1.232 2.312 1.00 96.82 7 A 1 ATOM 45 C C . THR A 1 7 ? -3.095 1.709 1.078 1.00 97.68 7 A 1 ATOM 46 O O . THR A 1 7 ? -3.549 1.518 -0.052 1.00 97.52 7 A 1 ATOM 47 C CB . THR A 1 7 ? -4.712 2.370 2.888 1.00 96.20 7 A 1 ATOM 48 O OG1 . THR A 1 7 ? -5.764 2.672 1.962 1.00 92.05 7 A 1 ATOM 49 C CG2 . THR A 1 7 ? -3.908 3.626 3.129 1.00 91.08 7 A 1 ATOM 50 N N . VAL A 1 8 ? -1.927 2.299 1.294 1.00 97.41 8 A 1 ATOM 51 C CA . VAL A 1 8 ? -1.099 2.776 0.189 1.00 97.61 8 A 1 ATOM 52 C C . VAL A 1 8 ? -0.616 1.600 -0.653 1.00 97.94 8 A 1 ATOM 53 O O . VAL A 1 8 ? -0.677 1.637 -1.883 1.00 97.54 8 A 1 ATOM 54 C CB . VAL A 1 8 ? 0.101 3.591 0.700 1.00 97.20 8 A 1 ATOM 55 C CG1 . VAL A 1 8 ? 1.090 3.871 -0.428 1.00 95.05 8 A 1 ATOM 56 C CG2 . VAL A 1 8 ? -0.374 4.901 1.307 1.00 94.86 8 A 1 ATOM 57 N N . LEU A 1 9 ? -0.153 0.555 0.010 1.00 97.39 9 A 1 ATOM 58 C CA . LEU A 1 9 ? 0.334 -0.633 -0.683 1.00 97.14 9 A 1 ATOM 59 C C . LEU A 1 9 ? -0.779 -1.280 -1.500 1.00 97.47 9 A 1 ATOM 60 O O . LEU A 1 9 ? -0.558 -1.711 -2.635 1.00 97.13 9 A 1 ATOM 61 C CB . LEU A 1 9 ? 0.893 -1.638 0.324 1.00 96.84 9 A 1 ATOM 62 C CG . LEU A 1 9 ? 2.227 -1.225 0.945 1.00 94.66 9 A 1 ATOM 63 C CD1 . LEU A 1 9 ? 2.582 -2.137 2.110 1.00 93.43 9 A 1 ATOM 64 C CD2 . LEU A 1 9 ? 3.336 -1.269 -0.104 1.00 92.84 9 A 1 ATOM 65 N N . LEU A 1 10 ? -1.977 -1.341 -0.931 1.00 97.30 10 A 1 ATOM 66 C CA . LEU A 1 10 ? -3.128 -1.903 -1.625 1.00 97.17 10 A 1 ATOM 67 C C . LEU A 1 10 ? -3.481 -1.070 -2.851 1.00 97.67 10 A 1 ATOM 68 O O . LEU A 1 10 ? -3.783 -1.614 -3.917 1.00 97.00 10 A 1 ATOM 69 C CB . LEU A 1 10 ? -4.326 -1.972 -0.675 1.00 96.68 10 A 1 ATOM 70 C CG . LEU A 1 10 ? -4.224 -3.085 0.366 1.00 94.27 10 A 1 ATOM 71 C CD1 . LEU A 1 10 ? -5.274 -2.903 1.453 1.00 92.15 10 A 1 ATOM 72 C CD2 . LEU A 1 10 ? -4.390 -4.444 -0.299 1.00 91.29 10 A 1 ATOM 73 N N . GLY A 1 11 ? -3.433 0.239 -2.697 1.00 96.42 11 A 1 ATOM 74 C CA . GLY A 1 11 ? -3.721 1.138 -3.807 1.00 96.34 11 A 1 ATOM 75 C C . GLY A 1 11 ? -2.714 0.994 -4.926 1.00 97.24 11 A 1 ATOM 76 O O . GLY A 1 11 ? -3.076 0.949 -6.105 1.00 97.05 11 A 1 ATOM 77 N N . VAL A 1 12 ? -1.443 0.901 -4.553 1.00 97.25 12 A 1 ATOM 78 C CA . VAL A 1 12 ? -0.366 0.745 -5.528 1.00 97.21 12 A 1 ATOM 79 C C . VAL A 1 12 ? -0.501 -0.581 -6.264 1.00 97.55 12 A 1 ATOM 80 O O . VAL A 1 12 ? -0.319 -0.649 -7.482 1.00 97.00 12 A 1 ATOM 81 C CB . VAL A 1 12 ? 1.013 0.826 -4.851 1.00 96.41 12 A 1 ATOM 82 C CG1 . VAL A 1 12 ? 2.124 0.520 -5.848 1.00 93.17 12 A 1 ATOM 83 C CG2 . VAL A 1 12 ? 1.223 2.206 -4.245 1.00 94.06 12 A 1 ATOM 84 N N . ALA A 1 13 ? -0.822 -1.635 -5.526 1.00 97.28 13 A 1 ATOM 85 C CA . ALA A 1 13 ? -0.995 -2.958 -6.118 1.00 97.00 13 A 1 ATOM 86 C C . ALA A 1 13 ? -2.138 -2.963 -7.129 1.00 97.51 13 A 1 ATOM 87 O O . ALA A 1 13 ? -2.023 -3.548 -8.206 1.00 96.86 13 A 1 ATOM 88 C CB . ALA A 1 13 ? -1.257 -3.988 -5.026 1.00 96.17 13 A 1 ATOM 89 N N . SER A 1 14 ? -3.237 -2.304 -6.790 1.00 97.34 14 A 1 ATOM 90 C CA . SER A 1 14 ? -4.393 -2.215 -7.678 1.00 97.07 14 A 1 ATOM 91 C C . SER A 1 14 ? -4.058 -1.431 -8.941 1.00 97.40 14 A 1 ATOM 92 O O . SER A 1 14 ? -4.466 -1.799 -10.044 1.00 96.81 14 A 1 ATOM 93 C CB . SER A 1 14 ? -5.565 -1.554 -6.958 1.00 96.02 14 A 1 ATOM 94 O OG . SER A 1 14 ? -5.970 -2.339 -5.855 1.00 86.38 14 A 1 ATOM 95 N N . ALA A 1 15 ? -3.296 -0.354 -8.776 1.00 96.76 15 A 1 ATOM 96 C CA . ALA A 1 15 ? -2.891 0.480 -9.903 1.00 96.53 15 A 1 ATOM 97 C C . ALA A 1 15 ? -1.912 -0.255 -10.809 1.00 96.85 15 A 1 ATOM 98 O O . ALA A 1 15 ? -1.909 -0.062 -12.026 1.00 95.56 15 A 1 ATOM 99 C CB . ALA A 1 15 ? -2.260 1.773 -9.397 1.00 95.27 15 A 1 ATOM 100 N N . ALA A 1 16 ? -1.070 -1.098 -10.209 1.00 96.14 16 A 1 ATOM 101 C CA . ALA A 1 16 ? -0.076 -1.863 -10.955 1.00 95.20 16 A 1 ATOM 102 C C . ALA A 1 16 ? -0.723 -2.971 -11.773 1.00 95.49 16 A 1 ATOM 103 O O . ALA A 1 16 ? -0.161 -3.427 -12.772 1.00 93.94 16 A 1 ATOM 104 C CB . ALA A 1 16 ? 0.955 -2.458 -10.002 1.00 93.40 16 A 1 ATOM 105 N N . SER A 1 17 ? -1.907 -3.398 -11.351 1.00 91.15 17 A 1 ATOM 106 C CA . SER A 1 17 ? -2.646 -4.461 -12.031 1.00 89.73 17 A 1 ATOM 107 C C . SER A 1 17 ? -3.173 -3.979 -13.390 1.00 87.63 17 A 1 ATOM 108 O O . SER A 1 17 ? -2.622 -4.383 -14.423 1.00 82.28 17 A 1 ATOM 109 C CB . SER A 1 17 ? -3.803 -4.950 -11.166 1.00 84.77 17 A 1 ATOM 110 O OG . SER A 1 17 ? -4.457 -6.038 -11.788 1.00 77.85 17 A 1 ATOM 111 O OXT . SER A 1 17 ? -4.119 -3.215 -13.415 1.00 77.84 17 A 1 #