# 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_spkb07814 # _entry.id spkb07814 # 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" "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" "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 LEU 2 1 n PRO 3 1 n SER 4 1 n ILE 5 1 n VAL 6 1 n ILE 7 1 n SER 8 1 n ILE 9 1 n VAL 10 1 n LEU 11 1 n ALA 12 1 n SER 13 1 n PHE 14 1 n VAL 15 1 n SER 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 @ 2025-07-03 18:35:53)" _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 95.57 _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 87.58 1 1 A LEU 2 2 92.26 1 2 A PRO 3 2 97.20 1 3 A SER 4 2 96.76 1 4 A ILE 5 2 96.24 1 5 A VAL 6 2 97.59 1 6 A ILE 7 2 96.45 1 7 A SER 8 2 96.85 1 8 A ILE 9 2 96.69 1 9 A VAL 10 2 97.67 1 10 A LEU 11 2 95.67 1 11 A ALA 12 2 98.17 1 12 A SER 13 2 97.36 1 13 A PHE 14 2 95.69 1 14 A VAL 15 2 96.74 1 15 A SER 16 2 95.72 1 16 A ALA 17 2 92.08 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 LEU . 2 A 2 A 3 1 n PRO . 3 A 3 A 4 1 n SER . 4 A 4 A 5 1 n ILE . 5 A 5 A 6 1 n VAL . 6 A 6 A 7 1 n ILE . 7 A 7 A 8 1 n SER . 8 A 8 A 9 1 n ILE . 9 A 9 A 10 1 n VAL . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n SER . 13 A 13 A 14 1 n PHE . 14 A 14 A 15 1 n VAL . 15 A 15 A 16 1 n SER . 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 ? -4.711 -7.725 8.908 1.00 92.63 1 A 1 ATOM 2 C CA . MET A 1 1 ? -3.878 -6.565 9.280 1.00 93.19 1 A 1 ATOM 3 C C . MET A 1 1 ? -2.901 -6.210 8.163 1.00 94.09 1 A 1 ATOM 4 O O . MET A 1 1 ? -2.419 -5.086 8.088 1.00 92.77 1 A 1 ATOM 5 C CB . MET A 1 1 ? -3.096 -6.873 10.562 1.00 88.99 1 A 1 ATOM 6 C CG . MET A 1 1 ? -4.023 -7.057 11.756 1.00 84.52 1 A 1 ATOM 7 S SD . MET A 1 1 ? -3.117 -7.476 13.253 1.00 81.59 1 A 1 ATOM 8 C CE . MET A 1 1 ? -4.464 -7.586 14.413 1.00 72.89 1 A 1 ATOM 9 N N . LEU A 1 2 ? -2.638 -7.161 7.295 1.00 93.67 2 A 1 ATOM 10 C CA . LEU A 1 2 ? -1.753 -6.937 6.155 1.00 95.88 2 A 1 ATOM 11 C C . LEU A 1 2 ? -2.271 -5.856 5.207 1.00 97.10 2 A 1 ATOM 12 O O . LEU A 1 2 ? -1.496 -5.009 4.763 1.00 96.38 2 A 1 ATOM 13 C CB . LEU A 1 2 ? -1.550 -8.246 5.390 1.00 93.90 2 A 1 ATOM 14 C CG . LEU A 1 2 ? -0.201 -8.894 5.646 1.00 89.93 2 A 1 ATOM 15 C CD1 . LEU A 1 2 ? -0.185 -9.540 7.027 1.00 87.16 2 A 1 ATOM 16 C CD2 . LEU A 1 2 ? 0.100 -9.926 4.574 1.00 84.09 2 A 1 ATOM 17 N N . PRO A 1 3 ? -3.578 -5.882 4.881 1.00 97.60 3 A 1 ATOM 18 C CA . PRO A 1 3 ? -4.128 -4.894 3.945 1.00 97.88 3 A 1 ATOM 19 C C . PRO A 1 3 ? -3.909 -3.456 4.406 1.00 98.25 3 A 1 ATOM 20 O O . PRO A 1 3 ? -3.605 -2.579 3.595 1.00 97.75 3 A 1 ATOM 21 C CB . PRO A 1 3 ? -5.626 -5.246 3.873 1.00 96.81 3 A 1 ATOM 22 C CG . PRO A 1 3 ? -5.891 -6.065 5.095 1.00 95.33 3 A 1 ATOM 23 C CD . PRO A 1 3 ? -4.611 -6.809 5.353 1.00 96.80 3 A 1 ATOM 24 N N . SER A 1 4 ? -4.062 -3.206 5.686 1.00 97.61 4 A 1 ATOM 25 C CA . SER A 1 4 ? -3.861 -1.860 6.222 1.00 98.06 4 A 1 ATOM 26 C C . SER A 1 4 ? -2.410 -1.416 6.041 1.00 98.34 4 A 1 ATOM 27 O O . SER A 1 4 ? -2.134 -0.255 5.743 1.00 97.64 4 A 1 ATOM 28 C CB . SER A 1 4 ? -4.243 -1.823 7.705 1.00 97.20 4 A 1 ATOM 29 O OG . SER A 1 4 ? -3.397 -2.647 8.462 1.00 91.71 4 A 1 ATOM 30 N N . ILE A 1 5 ? -1.491 -2.348 6.198 1.00 97.81 5 A 1 ATOM 31 C CA . ILE A 1 5 ? -0.065 -2.064 6.034 1.00 97.92 5 A 1 ATOM 32 C C . ILE A 1 5 ? 0.227 -1.698 4.582 1.00 98.24 5 A 1 ATOM 33 O O . ILE A 1 5 ? 0.980 -0.758 4.303 1.00 97.88 5 A 1 ATOM 34 C CB . ILE A 1 5 ? 0.789 -3.276 6.454 1.00 97.50 5 A 1 ATOM 35 C CG1 . ILE A 1 5 ? 0.578 -3.580 7.943 1.00 95.16 5 A 1 ATOM 36 C CG2 . ILE A 1 5 ? 2.270 -2.996 6.178 1.00 94.34 5 A 1 ATOM 37 C CD1 . ILE A 1 5 ? 1.160 -4.916 8.367 1.00 91.07 5 A 1 ATOM 38 N N . VAL A 1 6 ? -0.373 -2.435 3.669 1.00 98.08 6 A 1 ATOM 39 C CA . VAL A 1 6 ? -0.182 -2.185 2.242 1.00 98.20 6 A 1 ATOM 40 C C . VAL A 1 6 ? -0.644 -0.776 1.883 1.00 98.32 6 A 1 ATOM 41 O O . VAL A 1 6 ? 0.026 -0.066 1.129 1.00 98.10 6 A 1 ATOM 42 C CB . VAL A 1 6 ? -0.951 -3.220 1.407 1.00 97.84 6 A 1 ATOM 43 C CG1 . VAL A 1 6 ? -0.823 -2.916 -0.076 1.00 96.36 6 A 1 ATOM 44 C CG2 . VAL A 1 6 ? -0.433 -4.620 1.700 1.00 96.24 6 A 1 ATOM 45 N N . ILE A 1 7 ? -1.773 -0.372 2.421 1.00 98.01 7 A 1 ATOM 46 C CA . ILE A 1 7 ? -2.314 0.959 2.159 1.00 97.97 7 A 1 ATOM 47 C C . ILE A 1 7 ? -1.336 2.034 2.634 1.00 98.13 7 A 1 ATOM 48 O O . ILE A 1 7 ? -1.103 3.025 1.937 1.00 98.00 7 A 1 ATOM 49 C CB . ILE A 1 7 ? -3.674 1.129 2.855 1.00 97.81 7 A 1 ATOM 50 C CG1 . ILE A 1 7 ? -4.701 0.167 2.246 1.00 95.92 7 A 1 ATOM 51 C CG2 . ILE A 1 7 ? -4.165 2.570 2.714 1.00 95.26 7 A 1 ATOM 52 C CD1 . ILE A 1 7 ? -5.950 0.018 3.094 1.00 90.46 7 A 1 ATOM 53 N N . SER A 1 8 ? -0.769 1.836 3.795 1.00 98.18 8 A 1 ATOM 54 C CA . SER A 1 8 ? 0.191 2.793 4.345 1.00 98.27 8 A 1 ATOM 55 C C . SER A 1 8 ? 1.420 2.910 3.448 1.00 98.42 8 A 1 ATOM 56 O O . SER A 1 8 ? 1.920 4.005 3.196 1.00 97.97 8 A 1 ATOM 57 C CB . SER A 1 8 ? 0.615 2.360 5.745 1.00 97.84 8 A 1 ATOM 58 O OG . SER A 1 8 ? -0.495 2.341 6.617 1.00 90.42 8 A 1 ATOM 59 N N . ILE A 1 9 ? 1.889 1.776 2.952 1.00 97.89 9 A 1 ATOM 60 C CA . ILE A 1 9 ? 3.056 1.746 2.074 1.00 97.81 9 A 1 ATOM 61 C C . ILE A 1 9 ? 2.744 2.438 0.752 1.00 97.99 9 A 1 ATOM 62 O O . ILE A 1 9 ? 3.554 3.218 0.242 1.00 97.59 9 A 1 ATOM 63 C CB . ILE A 1 9 ? 3.505 0.297 1.816 1.00 97.62 9 A 1 ATOM 64 C CG1 . ILE A 1 9 ? 3.974 -0.351 3.123 1.00 96.21 9 A 1 ATOM 65 C CG2 . ILE A 1 9 ? 4.642 0.269 0.786 1.00 95.87 9 A 1 ATOM 66 C CD1 . ILE A 1 9 ? 4.114 -1.857 3.024 1.00 92.55 9 A 1 ATOM 67 N N . VAL A 1 10 ? 1.581 2.149 0.204 1.00 98.15 10 A 1 ATOM 68 C CA . VAL A 1 10 ? 1.166 2.750 -1.062 1.00 98.11 10 A 1 ATOM 69 C C . VAL A 1 10 ? 1.073 4.266 -0.926 1.00 98.20 10 A 1 ATOM 70 O O . VAL A 1 10 ? 1.528 5.006 -1.801 1.00 97.91 10 A 1 ATOM 71 C CB . VAL A 1 10 ? -0.185 2.177 -1.512 1.00 97.78 10 A 1 ATOM 72 C CG1 . VAL A 1 10 ? -0.705 2.914 -2.733 1.00 96.82 10 A 1 ATOM 73 C CG2 . VAL A 1 10 ? -0.047 0.695 -1.824 1.00 96.71 10 A 1 ATOM 74 N N . LEU A 1 11 ? 0.485 4.715 0.155 1.00 97.96 11 A 1 ATOM 75 C CA . LEU A 1 11 ? 0.328 6.146 0.393 1.00 97.79 11 A 1 ATOM 76 C C . LEU A 1 11 ? 1.687 6.824 0.514 1.00 97.90 11 A 1 ATOM 77 O O . LEU A 1 11 ? 1.927 7.873 -0.089 1.00 97.59 11 A 1 ATOM 78 C CB . LEU A 1 11 ? -0.497 6.361 1.660 1.00 97.41 11 A 1 ATOM 79 C CG . LEU A 1 11 ? -1.604 7.387 1.470 1.00 93.28 11 A 1 ATOM 80 C CD1 . LEU A 1 11 ? -2.864 6.941 2.195 1.00 91.49 11 A 1 ATOM 81 C CD2 . LEU A 1 11 ? -1.162 8.745 1.966 1.00 91.94 11 A 1 ATOM 82 N N . ALA A 1 12 ? 2.576 6.218 1.279 1.00 98.34 12 A 1 ATOM 83 C CA . ALA A 1 12 ? 3.925 6.757 1.448 1.00 98.29 12 A 1 ATOM 84 C C . ALA A 1 12 ? 4.664 6.794 0.116 1.00 98.39 12 A 1 ATOM 85 O O . ALA A 1 12 ? 5.371 7.757 -0.186 1.00 97.90 12 A 1 ATOM 86 C CB . ALA A 1 12 ? 4.692 5.906 2.450 1.00 97.92 12 A 1 ATOM 87 N N . SER A 1 13 ? 4.489 5.752 -0.683 1.00 98.35 13 A 1 ATOM 88 C CA . SER A 1 13 ? 5.121 5.666 -1.997 1.00 98.29 13 A 1 ATOM 89 C C . SER A 1 13 ? 4.588 6.751 -2.925 1.00 98.42 13 A 1 ATOM 90 O O . SER A 1 13 ? 5.351 7.398 -3.640 1.00 97.69 13 A 1 ATOM 91 C CB . SER A 1 13 ? 4.868 4.291 -2.601 1.00 97.72 13 A 1 ATOM 92 O OG . SER A 1 13 ? 5.354 4.236 -3.910 1.00 93.67 13 A 1 ATOM 93 N N . PHE A 1 14 ? 3.275 6.956 -2.908 1.00 98.10 14 A 1 ATOM 94 C CA . PHE A 1 14 ? 2.639 7.958 -3.756 1.00 98.05 14 A 1 ATOM 95 C C . PHE A 1 14 ? 3.119 9.361 -3.391 1.00 98.21 14 A 1 ATOM 96 O O . PHE A 1 14 ? 3.381 10.184 -4.265 1.00 97.50 14 A 1 ATOM 97 C CB . PHE A 1 14 ? 1.122 7.863 -3.607 1.00 97.52 14 A 1 ATOM 98 C CG . PHE A 1 14 ? 0.402 8.454 -4.790 1.00 95.97 14 A 1 ATOM 99 C CD1 . PHE A 1 14 ? 0.115 9.808 -4.838 1.00 93.48 14 A 1 ATOM 100 C CD2 . PHE A 1 14 ? 0.032 7.643 -5.854 1.00 94.12 14 A 1 ATOM 101 C CE1 . PHE A 1 14 ? -0.533 10.360 -5.936 1.00 93.22 14 A 1 ATOM 102 C CE2 . PHE A 1 14 ? -0.619 8.190 -6.957 1.00 93.06 14 A 1 ATOM 103 C CZ . PHE A 1 14 ? -0.900 9.547 -6.995 1.00 93.40 14 A 1 ATOM 104 N N . VAL A 1 15 ? 3.228 9.621 -2.109 1.00 98.20 15 A 1 ATOM 105 C CA . VAL A 1 15 ? 3.693 10.928 -1.643 1.00 98.03 15 A 1 ATOM 106 C C . VAL A 1 15 ? 5.147 11.161 -2.041 1.00 98.10 15 A 1 ATOM 107 O O . VAL A 1 15 ? 5.528 12.273 -2.417 1.00 97.47 15 A 1 ATOM 108 C CB . VAL A 1 15 ? 3.549 11.043 -0.118 1.00 97.22 15 A 1 ATOM 109 C CG1 . VAL A 1 15 ? 4.145 12.353 0.377 1.00 94.08 15 A 1 ATOM 110 C CG2 . VAL A 1 15 ? 2.090 10.958 0.278 1.00 94.11 15 A 1 ATOM 111 N N . SER A 1 16 ? 5.951 10.119 -1.956 1.00 97.83 16 A 1 ATOM 112 C CA . SER A 1 16 ? 7.365 10.212 -2.317 1.00 97.84 16 A 1 ATOM 113 C C . SER A 1 16 ? 7.549 10.322 -3.824 1.00 97.73 16 A 1 ATOM 114 O O . SER A 1 16 ? 8.445 11.028 -4.294 1.00 95.61 16 A 1 ATOM 115 C CB . SER A 1 16 ? 8.122 8.993 -1.803 1.00 96.49 16 A 1 ATOM 116 O OG . SER A 1 16 ? 8.053 8.925 -0.396 1.00 88.80 16 A 1 ATOM 117 N N . ALA A 1 17 ? 6.696 9.624 -4.559 1.00 96.06 17 A 1 ATOM 118 C CA . ALA A 1 17 ? 6.754 9.613 -6.023 1.00 94.96 17 A 1 ATOM 119 C C . ALA A 1 17 ? 5.949 10.765 -6.612 1.00 93.79 17 A 1 ATOM 120 O O . ALA A 1 17 ? 4.826 10.547 -7.082 1.00 91.20 17 A 1 ATOM 121 C CB . ALA A 1 17 ? 6.253 8.279 -6.541 1.00 92.18 17 A 1 ATOM 122 O OXT . ALA A 1 17 ? 6.460 11.903 -6.587 1.00 84.27 17 A 1 #