# 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_spkb28579 # _entry.id spkb28579 # 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 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" "C9 H11 N O2" 165.189 PHE y PHENYLALANINE c1ccc(cc1)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" "C4 H9 N O3" 119.119 THR y THREONINE C[C@H]([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 MET 1 1 n LEU 2 1 n LEU 3 1 n SER 4 1 n PHE 5 1 n LEU 6 1 n PRO 7 1 n LEU 8 1 n LEU 9 1 n PRO 10 1 n LEU 11 1 n ALA 12 1 n THR 13 1 n ALA 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 @ 2025-07-12 01:46:11)" _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 82.39 _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 77.37 1 1 A LEU 2 2 77.47 1 2 A LEU 3 2 81.38 1 3 A SER 4 2 84.73 1 4 A PHE 5 2 80.29 1 5 A LEU 6 2 82.01 1 6 A PRO 7 2 87.18 1 7 A LEU 8 2 82.42 1 8 A LEU 9 2 83.03 1 9 A PRO 10 2 88.87 1 10 A LEU 11 2 83.58 1 11 A ALA 12 2 87.62 1 12 A THR 13 2 81.65 1 13 A ALA 14 2 85.56 1 14 A ALA 15 2 77.19 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 LEU . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n SER . 4 A 4 A 5 1 n PHE . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n PRO . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n PRO . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n THR . 13 A 13 A 14 1 n ALA . 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 . MET A 1 1 ? -8.995 8.738 5.345 1.00 82.21 1 A 1 ATOM 2 C CA . MET A 1 1 ? -7.572 9.134 5.430 1.00 82.79 1 A 1 ATOM 3 C C . MET A 1 1 ? -6.703 8.203 4.579 1.00 83.73 1 A 1 ATOM 4 O O . MET A 1 1 ? -7.146 7.131 4.176 1.00 82.46 1 A 1 ATOM 5 C CB . MET A 1 1 ? -7.113 9.077 6.889 1.00 78.03 1 A 1 ATOM 6 C CG . MET A 1 1 ? -7.793 10.157 7.735 1.00 73.91 1 A 1 ATOM 7 S SD . MET A 1 1 ? -7.228 10.124 9.446 1.00 71.75 1 A 1 ATOM 8 C CE . MET A 1 1 ? -8.051 11.594 10.063 1.00 64.11 1 A 1 ATOM 9 N N . LEU A 1 2 ? -5.457 8.609 4.308 1.00 77.80 2 A 1 ATOM 10 C CA . LEU A 1 2 ? -4.523 7.812 3.501 1.00 80.54 2 A 1 ATOM 11 C C . LEU A 1 2 ? -4.043 6.568 4.251 1.00 83.71 2 A 1 ATOM 12 O O . LEU A 1 2 ? -3.441 5.680 3.654 1.00 81.89 2 A 1 ATOM 13 C CB . LEU A 1 2 ? -3.322 8.686 3.128 1.00 78.42 2 A 1 ATOM 14 C CG . LEU A 1 2 ? -3.655 9.765 2.099 1.00 74.50 2 A 1 ATOM 15 C CD1 . LEU A 1 2 ? -2.533 10.793 2.030 1.00 72.74 2 A 1 ATOM 16 C CD2 . LEU A 1 2 ? -3.847 9.122 0.719 1.00 70.15 2 A 1 ATOM 17 N N . LEU A 1 3 ? -4.304 6.501 5.544 1.00 83.77 3 A 1 ATOM 18 C CA . LEU A 1 3 ? -3.887 5.351 6.368 1.00 84.13 3 A 1 ATOM 19 C C . LEU A 1 3 ? -4.520 4.054 5.860 1.00 85.49 3 A 1 ATOM 20 O O . LEU A 1 3 ? -4.085 2.963 6.222 1.00 83.54 3 A 1 ATOM 21 C CB . LEU A 1 3 ? -4.288 5.603 7.829 1.00 82.48 3 A 1 ATOM 22 C CG . LEU A 1 3 ? -3.432 6.680 8.515 1.00 79.61 3 A 1 ATOM 23 C CD1 . LEU A 1 3 ? -4.113 7.150 9.804 1.00 76.65 3 A 1 ATOM 24 C CD2 . LEU A 1 3 ? -2.049 6.126 8.840 1.00 75.34 3 A 1 ATOM 25 N N . SER A 1 4 ? -5.537 4.170 5.009 1.00 86.18 4 A 1 ATOM 26 C CA . SER A 1 4 ? -6.222 2.997 4.455 1.00 86.50 4 A 1 ATOM 27 C C . SER A 1 4 ? -5.284 2.174 3.570 1.00 86.93 4 A 1 ATOM 28 O O . SER A 1 4 ? -5.452 0.962 3.436 1.00 84.94 4 A 1 ATOM 29 C CB . SER A 1 4 ? -7.442 3.447 3.654 1.00 85.15 4 A 1 ATOM 30 O OG . SER A 1 4 ? -8.297 4.249 4.456 1.00 78.69 4 A 1 ATOM 31 N N . PHE A 1 5 ? -4.277 2.827 2.972 1.00 83.08 5 A 1 ATOM 32 C CA . PHE A 1 5 ? -3.331 2.139 2.088 1.00 83.04 5 A 1 ATOM 33 C C . PHE A 1 5 ? -2.146 1.559 2.861 1.00 85.11 5 A 1 ATOM 34 O O . PHE A 1 5 ? -1.314 0.862 2.282 1.00 84.15 5 A 1 ATOM 35 C CB . PHE A 1 5 ? -2.824 3.117 1.023 1.00 82.02 5 A 1 ATOM 36 C CG . PHE A 1 5 ? -1.673 3.965 1.513 1.00 80.18 5 A 1 ATOM 37 C CD1 . PHE A 1 5 ? -1.903 5.131 2.225 1.00 78.07 5 A 1 ATOM 38 C CD2 . PHE A 1 5 ? -0.359 3.578 1.269 1.00 77.13 5 A 1 ATOM 39 C CE1 . PHE A 1 5 ? -0.844 5.910 2.693 1.00 77.06 5 A 1 ATOM 40 C CE2 . PHE A 1 5 ? 0.710 4.353 1.741 1.00 76.34 5 A 1 ATOM 41 C CZ . PHE A 1 5 ? 0.465 5.519 2.452 1.00 76.99 5 A 1 ATOM 42 N N . LEU A 1 6 ? -2.057 1.835 4.142 1.00 85.07 6 A 1 ATOM 43 C CA . LEU A 1 6 ? -0.945 1.360 4.975 1.00 84.63 6 A 1 ATOM 44 C C . LEU A 1 6 ? -0.744 -0.155 4.836 1.00 85.92 6 A 1 ATOM 45 O O . LEU A 1 6 ? 0.375 -0.609 4.584 1.00 84.94 6 A 1 ATOM 46 C CB . LEU A 1 6 ? -1.197 1.752 6.442 1.00 82.79 6 A 1 ATOM 47 C CG . LEU A 1 6 ? 0.081 2.061 7.218 1.00 79.83 6 A 1 ATOM 48 C CD1 . LEU A 1 6 ? -0.253 2.866 8.477 1.00 77.39 6 A 1 ATOM 49 C CD2 . LEU A 1 6 ? 0.796 0.776 7.610 1.00 75.51 6 A 1 ATOM 50 N N . PRO A 1 7 ? -1.811 -0.957 4.985 1.00 88.17 7 A 1 ATOM 51 C CA . PRO A 1 7 ? -1.683 -2.418 4.874 1.00 87.86 7 A 1 ATOM 52 C C . PRO A 1 7 ? -1.303 -2.878 3.470 1.00 88.94 7 A 1 ATOM 53 O O . PRO A 1 7 ? -0.703 -3.941 3.305 1.00 86.29 7 A 1 ATOM 54 C CB . PRO A 1 7 ? -3.081 -2.926 5.264 1.00 85.75 7 A 1 ATOM 55 C CG . PRO A 1 7 ? -3.988 -1.778 4.957 1.00 85.04 7 A 1 ATOM 56 C CD . PRO A 1 7 ? -3.179 -0.536 5.252 1.00 88.21 7 A 1 ATOM 57 N N . LEU A 1 8 ? -1.637 -2.090 2.455 1.00 84.79 8 A 1 ATOM 58 C CA . LEU A 1 8 ? -1.321 -2.438 1.068 1.00 84.84 8 A 1 ATOM 59 C C . LEU A 1 8 ? 0.080 -1.981 0.687 1.00 86.23 8 A 1 ATOM 60 O O . LEU A 1 8 ? 0.626 -2.440 -0.319 1.00 84.09 8 A 1 ATOM 61 C CB . LEU A 1 8 ? -2.349 -1.791 0.138 1.00 83.21 8 A 1 ATOM 62 C CG . LEU A 1 8 ? -3.713 -2.477 0.183 1.00 80.70 8 A 1 ATOM 63 C CD1 . LEU A 1 8 ? -4.754 -1.615 -0.523 1.00 79.24 8 A 1 ATOM 64 C CD2 . LEU A 1 8 ? -3.629 -3.843 -0.505 1.00 76.23 8 A 1 ATOM 65 N N . LEU A 1 9 ? 0.670 -1.101 1.480 1.00 85.66 9 A 1 ATOM 66 C CA . LEU A 1 9 ? 2.020 -0.599 1.207 1.00 85.95 9 A 1 ATOM 67 C C . LEU A 1 9 ? 3.029 -1.749 1.122 1.00 87.20 9 A 1 ATOM 68 O O . LEU A 1 9 ? 3.744 -1.878 0.126 1.00 85.95 9 A 1 ATOM 69 C CB . LEU A 1 9 ? 2.430 0.397 2.299 1.00 84.39 9 A 1 ATOM 70 C CG . LEU A 1 9 ? 3.764 1.083 2.023 1.00 80.54 9 A 1 ATOM 71 C CD1 . LEU A 1 9 ? 3.620 2.107 0.898 1.00 78.27 9 A 1 ATOM 72 C CD2 . LEU A 1 9 ? 4.253 1.775 3.295 1.00 76.32 9 A 1 ATOM 73 N N . PRO A 1 10 ? 3.119 -2.596 2.153 1.00 90.52 10 A 1 ATOM 74 C CA . PRO A 1 10 ? 4.061 -3.724 2.134 1.00 89.66 10 A 1 ATOM 75 C C . PRO A 1 10 ? 3.679 -4.770 1.097 1.00 90.32 10 A 1 ATOM 76 O O . PRO A 1 10 ? 4.546 -5.465 0.565 1.00 88.02 10 A 1 ATOM 77 C CB . PRO A 1 10 ? 3.961 -4.295 3.556 1.00 87.53 10 A 1 ATOM 78 C CG . PRO A 1 10 ? 2.603 -3.887 4.018 1.00 86.51 10 A 1 ATOM 79 C CD . PRO A 1 10 ? 2.352 -2.537 3.387 1.00 89.56 10 A 1 ATOM 80 N N . LEU A 1 11 ? 2.401 -4.900 0.798 1.00 88.40 11 A 1 ATOM 81 C CA . LEU A 1 11 ? 1.910 -5.867 -0.183 1.00 88.15 11 A 1 ATOM 82 C C . LEU A 1 11 ? 2.368 -5.469 -1.582 1.00 88.52 11 A 1 ATOM 83 O O . LEU A 1 11 ? 2.727 -6.317 -2.401 1.00 86.51 11 A 1 ATOM 84 C CB . LEU A 1 11 ? 0.378 -5.921 -0.123 1.00 85.57 11 A 1 ATOM 85 C CG . LEU A 1 11 ? -0.212 -7.304 -0.396 1.00 79.83 11 A 1 ATOM 86 C CD1 . LEU A 1 11 ? 0.332 -7.882 -1.693 1.00 76.90 11 A 1 ATOM 87 C CD2 . LEU A 1 11 ? 0.097 -8.231 0.766 1.00 74.77 11 A 1 ATOM 88 N N . ALA A 1 12 ? 2.359 -4.169 -1.858 1.00 88.31 12 A 1 ATOM 89 C CA . ALA A 1 12 ? 2.778 -3.655 -3.163 1.00 87.83 12 A 1 ATOM 90 C C . ALA A 1 12 ? 4.275 -3.855 -3.377 1.00 89.04 12 A 1 ATOM 91 O O . ALA A 1 12 ? 4.728 -4.021 -4.509 1.00 86.92 12 A 1 ATOM 92 C CB . ALA A 1 12 ? 2.426 -2.172 -3.264 1.00 86.00 12 A 1 ATOM 93 N N . THR A 1 13 ? 5.045 -3.835 -2.298 1.00 85.87 13 A 1 ATOM 94 C CA . THR A 1 13 ? 6.498 -4.011 -2.380 1.00 84.74 13 A 1 ATOM 95 C C . THR A 1 13 ? 6.851 -5.448 -2.752 1.00 84.04 13 A 1 ATOM 96 O O . THR A 1 13 ? 7.798 -5.693 -3.498 1.00 81.91 13 A 1 ATOM 97 C CB . THR A 1 13 ? 7.154 -3.655 -1.042 1.00 82.31 13 A 1 ATOM 98 O OG1 . THR A 1 13 ? 6.698 -2.372 -0.611 1.00 76.96 13 A 1 ATOM 99 C CG2 . THR A 1 13 ? 8.669 -3.605 -1.186 1.00 75.74 13 A 1 ATOM 100 N N . ALA A 1 14 ? 6.103 -6.400 -2.224 1.00 87.87 14 A 1 ATOM 101 C CA . ALA A 1 14 ? 6.340 -7.819 -2.499 1.00 86.20 14 A 1 ATOM 102 C C . ALA A 1 14 ? 5.708 -8.249 -3.822 1.00 86.27 14 A 1 ATOM 103 O O . ALA A 1 14 ? 6.313 -8.984 -4.601 1.00 83.77 14 A 1 ATOM 104 C CB . ALA A 1 14 ? 5.788 -8.656 -1.356 1.00 83.70 14 A 1 ATOM 105 N N . ALA A 1 15 ? 4.469 -7.789 -4.062 1.00 84.28 15 A 1 ATOM 106 C CA . ALA A 1 15 ? 3.735 -8.139 -5.277 1.00 80.91 15 A 1 ATOM 107 C C . ALA A 1 15 ? 2.839 -6.984 -5.719 1.00 78.24 15 A 1 ATOM 108 O O . ALA A 1 15 ? 2.129 -6.428 -4.874 1.00 74.70 15 A 1 ATOM 109 C CB . ALA A 1 15 ? 2.887 -9.374 -5.030 1.00 75.38 15 A 1 ATOM 110 O OXT . ALA A 1 15 ? 2.830 -6.653 -6.915 1.00 69.62 15 A 1 #