# 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_spkb28693 # _entry.id spkb28693 # 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" "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" "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 SER 3 1 n SER 4 1 n LEU 5 1 n LEU 6 1 n ALA 7 1 n GLY 8 1 n ALA 9 1 n GLY 10 1 n LEU 11 1 n VAL 12 1 n ALA 13 1 n LEU 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 @ 2025-07-12 21:43:14)" _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 91.07 _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 85.29 1 1 A LEU 2 2 85.78 1 2 A SER 3 2 87.53 1 3 A SER 4 2 88.98 1 4 A LEU 5 2 90.99 1 5 A LEU 6 2 89.54 1 6 A ALA 7 2 94.20 1 7 A GLY 8 2 95.19 1 8 A ALA 9 2 95.20 1 9 A GLY 10 2 95.33 1 10 A LEU 11 2 93.33 1 11 A VAL 12 2 93.96 1 12 A ALA 13 2 95.16 1 13 A LEU 14 2 92.46 1 14 A ALA 15 2 95.44 1 15 A ALA 16 2 95.39 1 16 A SER 17 2 84.20 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 SER . 3 A 3 A 4 1 n SER . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n GLY . 8 A 8 A 9 1 n ALA . 9 A 9 A 10 1 n GLY . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n VAL . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n LEU . 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 ? -7.546 -1.834 10.186 1.00 89.55 1 A 1 ATOM 2 C CA . MET A 1 1 ? -6.558 -2.935 10.235 1.00 90.84 1 A 1 ATOM 3 C C . MET A 1 1 ? -5.167 -2.417 9.849 1.00 91.67 1 A 1 ATOM 4 O O . MET A 1 1 ? -5.039 -1.591 8.945 1.00 90.44 1 A 1 ATOM 5 C CB . MET A 1 1 ? -6.965 -4.047 9.278 1.00 85.61 1 A 1 ATOM 6 C CG . MET A 1 1 ? -8.442 -4.431 9.396 1.00 82.28 1 A 1 ATOM 7 S SD . MET A 1 1 ? -8.864 -5.012 11.023 1.00 80.91 1 A 1 ATOM 8 C CE . MET A 1 1 ? -10.581 -5.401 10.793 1.00 70.99 1 A 1 ATOM 9 N N . LEU A 1 2 ? -4.140 -2.910 10.515 1.00 85.89 2 A 1 ATOM 10 C CA . LEU A 1 2 ? -2.750 -2.505 10.255 1.00 89.56 2 A 1 ATOM 11 C C . LEU A 1 2 ? -2.323 -2.834 8.824 1.00 92.69 2 A 1 ATOM 12 O O . LEU A 1 2 ? -1.551 -2.089 8.213 1.00 90.77 2 A 1 ATOM 13 C CB . LEU A 1 2 ? -1.836 -3.211 11.259 1.00 87.46 2 A 1 ATOM 14 C CG . LEU A 1 2 ? -1.520 -2.338 12.472 1.00 82.60 2 A 1 ATOM 15 C CD1 . LEU A 1 2 ? -1.511 -3.169 13.752 1.00 79.99 2 A 1 ATOM 16 C CD2 . LEU A 1 2 ? -0.175 -1.656 12.281 1.00 77.31 2 A 1 ATOM 17 N N . SER A 1 3 ? -2.841 -3.941 8.286 1.00 88.50 3 A 1 ATOM 18 C CA . SER A 1 3 ? -2.526 -4.366 6.915 1.00 90.24 3 A 1 ATOM 19 C C . SER A 1 3 ? -2.967 -3.317 5.895 1.00 92.40 3 A 1 ATOM 20 O O . SER A 1 3 ? -2.259 -3.036 4.923 1.00 88.83 3 A 1 ATOM 21 C CB . SER A 1 3 ? -3.197 -5.708 6.638 1.00 86.74 3 A 1 ATOM 22 O OG . SER A 1 3 ? -2.494 -6.421 5.656 1.00 78.46 3 A 1 ATOM 23 N N . SER A 1 4 ? -4.136 -2.717 6.127 1.00 89.30 4 A 1 ATOM 24 C CA . SER A 1 4 ? -4.672 -1.678 5.245 1.00 91.44 4 A 1 ATOM 25 C C . SER A 1 4 ? -3.800 -0.426 5.292 1.00 93.62 4 A 1 ATOM 26 O O . SER A 1 4 ? -3.559 0.216 4.267 1.00 90.61 4 A 1 ATOM 27 C CB . SER A 1 4 ? -6.104 -1.339 5.650 1.00 88.70 4 A 1 ATOM 28 O OG . SER A 1 4 ? -7.023 -2.083 4.877 1.00 80.24 4 A 1 ATOM 29 N N . LEU A 1 5 ? -3.312 -0.085 6.476 1.00 92.03 5 A 1 ATOM 30 C CA . LEU A 1 5 ? -2.445 1.084 6.649 1.00 93.50 5 A 1 ATOM 31 C C . LEU A 1 5 ? -1.128 0.889 5.898 1.00 95.15 5 A 1 ATOM 32 O O . LEU A 1 5 ? -0.610 1.826 5.284 1.00 93.56 5 A 1 ATOM 33 C CB . LEU A 1 5 ? -2.184 1.306 8.139 1.00 92.48 5 A 1 ATOM 34 C CG . LEU A 1 5 ? -3.405 1.848 8.891 1.00 89.36 5 A 1 ATOM 35 C CD1 . LEU A 1 5 ? -3.164 1.790 10.392 1.00 86.89 5 A 1 ATOM 36 C CD2 . LEU A 1 5 ? -3.687 3.292 8.473 1.00 84.95 5 A 1 ATOM 37 N N . LEU A 1 6 ? -0.606 -0.326 5.936 1.00 92.91 6 A 1 ATOM 38 C CA . LEU A 1 6 ? 0.635 -0.646 5.225 1.00 93.30 6 A 1 ATOM 39 C C . LEU A 1 6 ? 0.449 -0.501 3.718 1.00 94.39 6 A 1 ATOM 40 O O . LEU A 1 6 ? 1.337 0.004 3.023 1.00 93.34 6 A 1 ATOM 41 C CB . LEU A 1 6 ? 1.061 -2.071 5.574 1.00 91.61 6 A 1 ATOM 42 C CG . LEU A 1 6 ? 1.942 -2.140 6.818 1.00 85.13 6 A 1 ATOM 43 C CD1 . LEU A 1 6 ? 1.986 -3.562 7.360 1.00 83.30 6 A 1 ATOM 44 C CD2 . LEU A 1 6 ? 3.352 -1.662 6.490 1.00 82.35 6 A 1 ATOM 45 N N . ALA A 1 7 ? -0.714 -0.924 3.216 1.00 94.30 7 A 1 ATOM 46 C CA . ALA A 1 7 ? -1.024 -0.810 1.791 1.00 94.53 7 A 1 ATOM 47 C C . ALA A 1 7 ? -1.058 0.658 1.366 1.00 95.62 7 A 1 ATOM 48 O O . ALA A 1 7 ? -0.580 1.013 0.284 1.00 93.53 7 A 1 ATOM 49 C CB . ALA A 1 7 ? -2.359 -1.491 1.507 1.00 93.00 7 A 1 ATOM 50 N N . GLY A 1 8 ? -1.611 1.508 2.226 1.00 94.39 8 A 1 ATOM 51 C CA . GLY A 1 8 ? -1.669 2.942 1.949 1.00 94.81 8 A 1 ATOM 52 C C . GLY A 1 8 ? -0.280 3.547 1.861 1.00 96.14 8 A 1 ATOM 53 O O . GLY A 1 8 ? -0.006 4.374 0.987 1.00 95.43 8 A 1 ATOM 54 N N . ALA A 1 9 ? 0.606 3.117 2.746 1.00 95.33 9 A 1 ATOM 55 C CA . ALA A 1 9 ? 1.987 3.601 2.749 1.00 95.47 9 A 1 ATOM 56 C C . ALA A 1 9 ? 2.700 3.212 1.458 1.00 96.46 9 A 1 ATOM 57 O O . ALA A 1 9 ? 3.509 3.980 0.931 1.00 94.85 9 A 1 ATOM 58 C CB . ALA A 1 9 ? 2.721 3.028 3.956 1.00 93.91 9 A 1 ATOM 59 N N . GLY A 1 10 ? 2.395 2.030 0.944 1.00 94.19 10 A 1 ATOM 60 C CA . GLY A 1 10 ? 2.991 1.568 -0.310 1.00 94.83 10 A 1 ATOM 61 C C . GLY A 1 10 ? 2.587 2.439 -1.484 1.00 96.30 10 A 1 ATOM 62 O O . GLY A 1 10 ? 3.410 2.755 -2.348 1.00 96.02 10 A 1 ATOM 63 N N . LEU A 1 11 ? 1.316 2.841 -1.508 1.00 94.69 11 A 1 ATOM 64 C CA . LEU A 1 11 ? 0.814 3.708 -2.575 1.00 95.22 11 A 1 ATOM 65 C C . LEU A 1 11 ? 1.492 5.073 -2.523 1.00 96.45 11 A 1 ATOM 66 O O . LEU A 1 11 ? 1.821 5.647 -3.567 1.00 95.56 11 A 1 ATOM 67 C CB . LEU A 1 11 ? -0.699 3.866 -2.437 1.00 93.88 11 A 1 ATOM 68 C CG . LEU A 1 11 ? -1.490 2.704 -3.031 1.00 91.46 11 A 1 ATOM 69 C CD1 . LEU A 1 11 ? -2.958 2.838 -2.682 1.00 90.38 11 A 1 ATOM 70 C CD2 . LEU A 1 11 ? -1.326 2.667 -4.549 1.00 88.98 11 A 1 ATOM 71 N N . VAL A 1 12 ? 1.703 5.581 -1.322 1.00 94.82 12 A 1 ATOM 72 C CA . VAL A 1 12 ? 2.373 6.871 -1.145 1.00 95.17 12 A 1 ATOM 73 C C . VAL A 1 12 ? 3.805 6.791 -1.667 1.00 95.88 12 A 1 ATOM 74 O O . VAL A 1 12 ? 4.291 7.723 -2.315 1.00 95.28 12 A 1 ATOM 75 C CB . VAL A 1 12 ? 2.362 7.287 0.332 1.00 93.71 12 A 1 ATOM 76 C CG1 . VAL A 1 12 ? 3.159 8.568 0.539 1.00 91.09 12 A 1 ATOM 77 C CG2 . VAL A 1 12 ? 0.931 7.488 0.814 1.00 91.76 12 A 1 ATOM 78 N N . ALA A 1 13 ? 4.472 5.681 -1.404 1.00 95.34 13 A 1 ATOM 79 C CA . ALA A 1 13 ? 5.845 5.480 -1.869 1.00 95.44 13 A 1 ATOM 80 C C . ALA A 1 13 ? 5.901 5.460 -3.397 1.00 96.23 13 A 1 ATOM 81 O O . ALA A 1 13 ? 6.818 6.026 -3.995 1.00 94.61 13 A 1 ATOM 82 C CB . ALA A 1 13 ? 6.392 4.180 -1.299 1.00 94.18 13 A 1 ATOM 83 N N . LEU A 1 14 ? 4.913 4.824 -4.029 1.00 95.25 14 A 1 ATOM 84 C CA . LEU A 1 14 ? 4.840 4.763 -5.491 1.00 95.27 14 A 1 ATOM 85 C C . LEU A 1 14 ? 4.607 6.149 -6.078 1.00 96.16 14 A 1 ATOM 86 O O . LEU A 1 14 ? 5.217 6.510 -7.091 1.00 95.13 14 A 1 ATOM 87 C CB . LEU A 1 14 ? 3.711 3.820 -5.903 1.00 93.70 14 A 1 ATOM 88 C CG . LEU A 1 14 ? 4.174 2.369 -6.033 1.00 89.56 14 A 1 ATOM 89 C CD1 . LEU A 1 14 ? 2.998 1.420 -5.916 1.00 87.90 14 A 1 ATOM 90 C CD2 . LEU A 1 14 ? 4.885 2.165 -7.364 1.00 86.74 14 A 1 ATOM 91 N N . ALA A 1 15 ? 3.727 6.918 -5.447 1.00 95.74 15 A 1 ATOM 92 C CA . ALA A 1 15 ? 3.425 8.272 -5.906 1.00 95.86 15 A 1 ATOM 93 C C . ALA A 1 15 ? 4.630 9.191 -5.726 1.00 96.21 15 A 1 ATOM 94 O O . ALA A 1 15 ? 4.852 10.096 -6.536 1.00 94.81 15 A 1 ATOM 95 C CB . ALA A 1 15 ? 2.223 8.815 -5.139 1.00 94.58 15 A 1 ATOM 96 N N . ALA A 1 16 ? 5.398 8.973 -4.672 1.00 96.30 16 A 1 ATOM 97 C CA . ALA A 1 16 ? 6.582 9.781 -4.387 1.00 95.85 16 A 1 ATOM 98 C C . ALA A 1 16 ? 7.744 9.407 -5.301 1.00 95.96 16 A 1 ATOM 99 O O . ALA A 1 16 ? 8.628 10.231 -5.554 1.00 94.43 16 A 1 ATOM 100 C CB . ALA A 1 16 ? 6.986 9.604 -2.927 1.00 94.41 16 A 1 ATOM 101 N N . SER A 1 17 ? 7.743 8.169 -5.793 1.00 91.22 17 A 1 ATOM 102 C CA . SER A 1 17 ? 8.806 7.673 -6.675 1.00 89.05 17 A 1 ATOM 103 C C . SER A 1 17 ? 8.785 8.393 -8.020 1.00 86.02 17 A 1 ATOM 104 O O . SER A 1 17 ? 9.857 8.735 -8.537 1.00 82.40 17 A 1 ATOM 105 C CB . SER A 1 17 ? 8.654 6.165 -6.884 1.00 83.65 17 A 1 ATOM 106 O OG . SER A 1 17 ? 9.203 5.459 -5.797 1.00 78.10 17 A 1 ATOM 107 O OXT . SER A 1 17 ? 7.705 8.581 -8.571 1.00 78.94 17 A 1 #