# 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_spkb08747 # _entry.id spkb08747 # 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 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" "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 GLY 3 1 n ILE 4 1 n ILE 5 1 n LEU 6 1 n ALA 7 1 n LEU 8 1 n VAL 9 1 n LEU 10 1 n THR 11 1 n LEU 12 1 n VAL 13 1 n GLY 14 1 n SER 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 @ 2025-07-07 18:53:33)" _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 95.70 _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 91.89 1 1 A ARG 2 2 91.00 1 2 A GLY 3 2 98.45 1 3 A ILE 4 2 97.47 1 4 A ILE 5 2 97.70 1 5 A LEU 6 2 96.39 1 6 A ALA 7 2 98.55 1 7 A LEU 8 2 97.32 1 8 A VAL 9 2 98.13 1 9 A LEU 10 2 97.20 1 10 A THR 11 2 97.46 1 11 A LEU 12 2 96.98 1 12 A VAL 13 2 97.22 1 13 A GLY 14 2 96.81 1 14 A SER 15 2 87.45 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 MET . 1 A 1 A 2 1 n ARG . 2 A 2 A 3 1 n GLY . 3 A 3 A 4 1 n ILE . 4 A 4 A 5 1 n ILE . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n VAL . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n THR . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n VAL . 13 A 13 A 14 1 n GLY . 14 A 14 A 15 1 n SER . 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 . MET A 1 1 ? -6.607 -6.551 6.949 1.00 96.05 1 A 1 ATOM 2 C CA . MET A 1 1 ? -5.623 -5.514 7.301 1.00 96.85 1 A 1 ATOM 3 C C . MET A 1 1 ? -5.128 -4.801 6.044 1.00 97.04 1 A 1 ATOM 4 O O . MET A 1 1 ? -4.195 -5.255 5.389 1.00 95.63 1 A 1 ATOM 5 C CB . MET A 1 1 ? -4.433 -6.137 8.019 1.00 94.76 1 A 1 ATOM 6 C CG . MET A 1 1 ? -4.820 -6.823 9.314 1.00 90.67 1 A 1 ATOM 7 S SD . MET A 1 1 ? -3.438 -7.682 10.068 1.00 87.97 1 A 1 ATOM 8 C CE . MET A 1 1 ? -4.224 -8.353 11.517 1.00 76.13 1 A 1 ATOM 9 N N . ARG A 1 2 ? -5.756 -3.687 5.711 1.00 97.43 2 A 1 ATOM 10 C CA . ARG A 1 2 ? -5.388 -2.927 4.520 1.00 98.08 2 A 1 ATOM 11 C C . ARG A 1 2 ? -4.705 -1.612 4.874 1.00 98.38 2 A 1 ATOM 12 O O . ARG A 1 2 ? -4.054 -1.003 4.027 1.00 97.83 2 A 1 ATOM 13 C CB . ARG A 1 2 ? -6.637 -2.642 3.681 1.00 97.32 2 A 1 ATOM 14 C CG . ARG A 1 2 ? -7.448 -3.881 3.376 1.00 93.60 2 A 1 ATOM 15 C CD . ARG A 1 2 ? -8.901 -3.670 3.780 1.00 91.22 2 A 1 ATOM 16 N NE . ARG A 1 2 ? -9.811 -3.949 2.674 1.00 86.31 2 A 1 ATOM 17 C CZ . ARG A 1 2 ? -11.113 -3.713 2.693 1.00 85.13 2 A 1 ATOM 18 N NH1 . ARG A 1 2 ? -11.684 -3.199 3.764 1.00 77.49 2 A 1 ATOM 19 N NH2 . ARG A 1 2 ? -11.858 -3.991 1.637 1.00 78.22 2 A 1 ATOM 20 N N . GLY A 1 3 ? -4.850 -1.179 6.114 1.00 98.11 3 A 1 ATOM 21 C CA . GLY A 1 3 ? -4.234 0.069 6.557 1.00 98.50 3 A 1 ATOM 22 C C . GLY A 1 3 ? -2.730 0.083 6.337 1.00 98.70 3 A 1 ATOM 23 O O . GLY A 1 3 ? -2.157 1.088 5.917 1.00 98.51 3 A 1 ATOM 24 N N . ILE A 1 4 ? -2.096 -1.043 6.607 1.00 98.56 4 A 1 ATOM 25 C CA . ILE A 1 4 ? -0.651 -1.174 6.421 1.00 98.63 4 A 1 ATOM 26 C C . ILE A 1 4 ? -0.279 -1.047 4.950 1.00 98.72 4 A 1 ATOM 27 O O . ILE A 1 4 ? 0.693 -0.379 4.590 1.00 98.52 4 A 1 ATOM 28 C CB . ILE A 1 4 ? -0.146 -2.518 6.964 1.00 98.49 4 A 1 ATOM 29 C CG1 . ILE A 1 4 ? -0.638 -2.728 8.397 1.00 97.00 4 A 1 ATOM 30 C CG2 . ILE A 1 4 ? 1.372 -2.581 6.889 1.00 96.62 4 A 1 ATOM 31 C CD1 . ILE A 1 4 ? -0.224 -1.611 9.337 1.00 93.24 4 A 1 ATOM 32 N N . ILE A 1 5 ? -1.055 -1.708 4.108 1.00 98.66 5 A 1 ATOM 33 C CA . ILE A 1 5 ? -0.815 -1.681 2.669 1.00 98.66 5 A 1 ATOM 34 C C . ILE A 1 5 ? -0.955 -0.262 2.135 1.00 98.68 5 A 1 ATOM 35 O O . ILE A 1 5 ? -0.141 0.204 1.332 1.00 98.57 5 A 1 ATOM 36 C CB . ILE A 1 5 ? -1.795 -2.607 1.935 1.00 98.59 5 A 1 ATOM 37 C CG1 . ILE A 1 5 ? -1.752 -4.013 2.534 1.00 97.58 5 A 1 ATOM 38 C CG2 . ILE A 1 5 ? -1.463 -2.635 0.446 1.00 97.43 5 A 1 ATOM 39 C CD1 . ILE A 1 5 ? -0.375 -4.641 2.480 1.00 93.40 5 A 1 ATOM 40 N N . LEU A 1 6 ? -1.992 0.417 2.587 1.00 98.62 6 A 1 ATOM 41 C CA . LEU A 1 6 ? -2.247 1.788 2.160 1.00 98.62 6 A 1 ATOM 42 C C . LEU A 1 6 ? -1.095 2.708 2.549 1.00 98.70 6 A 1 ATOM 43 O O . LEU A 1 6 ? -0.665 3.554 1.762 1.00 98.62 6 A 1 ATOM 44 C CB . LEU A 1 6 ? -3.546 2.292 2.782 1.00 98.42 6 A 1 ATOM 45 C CG . LEU A 1 6 ? -4.008 3.647 2.268 1.00 93.98 6 A 1 ATOM 46 C CD1 . LEU A 1 6 ? -4.332 3.576 0.787 1.00 91.50 6 A 1 ATOM 47 C CD2 . LEU A 1 6 ? -5.211 4.129 3.063 1.00 92.64 6 A 1 ATOM 48 N N . ALA A 1 7 ? -0.598 2.539 3.766 1.00 98.54 7 A 1 ATOM 49 C CA . ALA A 1 7 ? 0.517 3.344 4.257 1.00 98.58 7 A 1 ATOM 50 C C . ALA A 1 7 ? 1.774 3.112 3.428 1.00 98.67 7 A 1 ATOM 51 O O . ALA A 1 7 ? 2.505 4.054 3.113 1.00 98.53 7 A 1 ATOM 52 C CB . ALA A 1 7 ? 0.792 3.010 5.716 1.00 98.44 7 A 1 ATOM 53 N N . LEU A 1 8 ? 2.011 1.862 3.080 1.00 98.58 8 A 1 ATOM 54 C CA . LEU A 1 8 ? 3.175 1.497 2.278 1.00 98.56 8 A 1 ATOM 55 C C . LEU A 1 8 ? 3.108 2.129 0.894 1.00 98.67 8 A 1 ATOM 56 O O . LEU A 1 8 ? 4.085 2.701 0.413 1.00 98.59 8 A 1 ATOM 57 C CB . LEU A 1 8 ? 3.259 -0.021 2.143 1.00 98.41 8 A 1 ATOM 58 C CG . LEU A 1 8 ? 4.484 -0.514 1.393 1.00 96.24 8 A 1 ATOM 59 C CD1 . LEU A 1 8 ? 5.752 -0.185 2.161 1.00 94.54 8 A 1 ATOM 60 C CD2 . LEU A 1 8 ? 4.386 -2.009 1.139 1.00 94.94 8 A 1 ATOM 61 N N . VAL A 1 9 ? 1.949 2.025 0.265 1.00 98.58 9 A 1 ATOM 62 C CA . VAL A 1 9 ? 1.754 2.593 -1.066 1.00 98.56 9 A 1 ATOM 63 C C . VAL A 1 9 ? 1.870 4.112 -1.027 1.00 98.61 9 A 1 ATOM 64 O O . VAL A 1 9 ? 2.439 4.728 -1.931 1.00 98.45 9 A 1 ATOM 65 C CB . VAL A 1 9 ? 0.384 2.200 -1.637 1.00 98.34 9 A 1 ATOM 66 C CG1 . VAL A 1 9 ? 0.145 2.873 -2.979 1.00 97.23 9 A 1 ATOM 67 C CG2 . VAL A 1 9 ? 0.286 0.688 -1.772 1.00 97.13 9 A 1 ATOM 68 N N . LEU A 1 10 ? 1.336 4.708 0.028 1.00 98.67 10 A 1 ATOM 69 C CA . LEU A 1 10 ? 1.368 6.159 0.187 1.00 98.56 10 A 1 ATOM 70 C C . LEU A 1 10 ? 2.799 6.682 0.244 1.00 98.63 10 A 1 ATOM 71 O O . LEU A 1 10 ? 3.139 7.655 -0.431 1.00 98.33 10 A 1 ATOM 72 C CB . LEU A 1 10 ? 0.622 6.559 1.457 1.00 98.21 10 A 1 ATOM 73 C CG . LEU A 1 10 ? 0.559 8.059 1.709 1.00 96.33 10 A 1 ATOM 74 C CD1 . LEU A 1 10 ? -0.234 8.756 0.615 1.00 94.46 10 A 1 ATOM 75 C CD2 . LEU A 1 10 ? -0.052 8.341 3.071 1.00 94.38 10 A 1 ATOM 76 N N . THR A 1 11 ? 3.636 6.050 1.056 1.00 98.65 11 A 1 ATOM 77 C CA . THR A 1 11 ? 5.027 6.472 1.189 1.00 98.59 11 A 1 ATOM 78 C C . THR A 1 11 ? 5.798 6.258 -0.107 1.00 98.65 11 A 1 ATOM 79 O O . THR A 1 11 ? 6.652 7.068 -0.466 1.00 98.23 11 A 1 ATOM 80 C CB . THR A 1 11 ? 5.724 5.732 2.339 1.00 98.24 11 A 1 ATOM 81 O OG1 . THR A 1 11 ? 7.046 6.250 2.500 1.00 95.50 11 A 1 ATOM 82 C CG2 . THR A 1 11 ? 5.807 4.250 2.080 1.00 94.35 11 A 1 ATOM 83 N N . LEU A 1 12 ? 5.484 5.173 -0.814 1.00 98.62 12 A 1 ATOM 84 C CA . LEU A 1 12 ? 6.147 4.855 -2.074 1.00 98.56 12 A 1 ATOM 85 C C . LEU A 1 12 ? 5.815 5.900 -3.132 1.00 98.57 12 A 1 ATOM 86 O O . LEU A 1 12 ? 6.700 6.403 -3.828 1.00 98.01 12 A 1 ATOM 87 C CB . LEU A 1 12 ? 5.718 3.464 -2.559 1.00 98.32 12 A 1 ATOM 88 C CG . LEU A 1 12 ? 6.762 2.719 -3.384 1.00 96.50 12 A 1 ATOM 89 C CD1 . LEU A 1 12 ? 7.134 3.486 -4.635 1.00 93.75 12 A 1 ATOM 90 C CD2 . LEU A 1 12 ? 7.992 2.443 -2.533 1.00 93.53 12 A 1 ATOM 91 N N . VAL A 1 13 ? 4.538 6.226 -3.248 1.00 98.64 13 A 1 ATOM 92 C CA . VAL A 1 13 ? 4.083 7.212 -4.224 1.00 98.50 13 A 1 ATOM 93 C C . VAL A 1 13 ? 4.525 8.618 -3.832 1.00 98.40 13 A 1 ATOM 94 O O . VAL A 1 13 ? 4.838 9.450 -4.686 1.00 96.85 13 A 1 ATOM 95 C CB . VAL A 1 13 ? 2.553 7.172 -4.367 1.00 97.81 13 A 1 ATOM 96 C CG1 . VAL A 1 13 ? 2.078 8.251 -5.324 1.00 94.42 13 A 1 ATOM 97 C CG2 . VAL A 1 13 ? 2.104 5.804 -4.845 1.00 95.92 13 A 1 ATOM 98 N N . GLY A 1 14 ? 4.535 8.887 -2.543 1.00 97.74 14 A 1 ATOM 99 C CA . GLY A 1 14 ? 4.926 10.197 -2.041 1.00 97.23 14 A 1 ATOM 100 C C . GLY A 1 14 ? 6.417 10.460 -2.160 1.00 96.99 14 A 1 ATOM 101 O O . GLY A 1 14 ? 6.847 11.611 -2.210 1.00 95.28 14 A 1 ATOM 102 N N . SER A 1 15 ? 7.209 9.391 -2.198 1.00 95.09 15 A 1 ATOM 103 C CA . SER A 1 15 ? 8.669 9.502 -2.295 1.00 93.32 15 A 1 ATOM 104 C C . SER A 1 15 ? 9.110 9.975 -3.679 1.00 90.58 15 A 1 ATOM 105 O O . SER A 1 15 ? 9.661 11.082 -3.783 1.00 83.79 15 A 1 ATOM 106 C CB . SER A 1 15 ? 9.324 8.159 -1.974 1.00 88.36 15 A 1 ATOM 107 O OG . SER A 1 15 ? 9.138 7.823 -0.618 1.00 79.27 15 A 1 ATOM 108 O OXT . SER A 1 15 ? 8.942 9.226 -4.655 1.00 81.73 15 A 1 #