# 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_spkb34829 # _entry.id spkb34829 # 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 ALA 2 1 n VAL 3 1 n PRO 4 1 n SER 5 1 n VAL 6 1 n MET 7 1 n VAL 8 1 n LEU 9 1 n PRO 10 1 n LEU 11 1 n LEU 12 1 n ILE 13 1 n VAL 14 1 n VAL 15 1 n PHE 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 @ 2025-07-13 00:48:22)" _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 93.05 _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 75.63 1 1 A ALA 2 2 83.52 1 2 A VAL 3 2 87.19 1 3 A PRO 4 2 94.01 1 4 A SER 5 2 93.94 1 5 A VAL 6 2 94.59 1 6 A MET 7 2 92.37 1 7 A VAL 8 2 96.14 1 8 A LEU 9 2 94.83 1 9 A PRO 10 2 97.05 1 10 A LEU 11 2 95.23 1 11 A LEU 12 2 95.42 1 12 A ILE 13 2 96.78 1 13 A VAL 14 2 97.25 1 14 A VAL 15 2 96.81 1 15 A PHE 16 2 94.95 1 16 A ALA 17 2 93.60 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 ALA . 2 A 2 A 3 1 n VAL . 3 A 3 A 4 1 n PRO . 4 A 4 A 5 1 n SER . 5 A 5 A 6 1 n VAL . 6 A 6 A 7 1 n MET . 7 A 7 A 8 1 n VAL . 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 LEU . 12 A 12 A 13 1 n ILE . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n VAL . 15 A 15 A 16 1 n PHE . 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 ? -7.353 7.887 -7.823 1.00 79.43 1 A 1 ATOM 2 C CA . MET A 1 1 ? -7.317 7.153 -6.545 1.00 79.82 1 A 1 ATOM 3 C C . MET A 1 1 ? -6.896 8.070 -5.406 1.00 81.36 1 A 1 ATOM 4 O O . MET A 1 1 ? -6.051 8.932 -5.592 1.00 79.49 1 A 1 ATOM 5 C CB . MET A 1 1 ? -6.337 5.988 -6.638 1.00 76.67 1 A 1 ATOM 6 C CG . MET A 1 1 ? -6.792 4.947 -7.639 1.00 73.67 1 A 1 ATOM 7 S SD . MET A 1 1 ? -5.651 3.568 -7.738 1.00 69.98 1 A 1 ATOM 8 C CE . MET A 1 1 ? -6.450 2.592 -8.997 1.00 64.61 1 A 1 ATOM 9 N N . ALA A 1 2 ? -7.495 7.874 -4.234 1.00 79.61 2 A 1 ATOM 10 C CA . ALA A 1 2 ? -7.209 8.723 -3.077 1.00 84.82 2 A 1 ATOM 11 C C . ALA A 1 2 ? -6.210 8.062 -2.125 1.00 87.55 2 A 1 ATOM 12 O O . ALA A 1 2 ? -6.083 8.460 -0.974 1.00 84.37 2 A 1 ATOM 13 C CB . ALA A 1 2 ? -8.502 9.055 -2.339 1.00 81.24 2 A 1 ATOM 14 N N . VAL A 1 3 ? -5.502 7.057 -2.609 1.00 87.81 3 A 1 ATOM 15 C CA . VAL A 1 3 ? -4.518 6.343 -1.789 1.00 90.47 3 A 1 ATOM 16 C C . VAL A 1 3 ? -5.104 5.860 -0.461 1.00 92.57 3 A 1 ATOM 17 O O . VAL A 1 3 ? -4.650 6.263 0.610 1.00 91.30 3 A 1 ATOM 18 C CB . VAL A 1 3 ? -3.317 7.249 -1.496 1.00 87.26 3 A 1 ATOM 19 C CG1 . VAL A 1 3 ? -2.219 6.438 -0.827 1.00 79.62 3 A 1 ATOM 20 C CG2 . VAL A 1 3 ? -2.811 7.874 -2.772 1.00 81.30 3 A 1 ATOM 21 N N . PRO A 1 4 ? -6.116 5.004 -0.510 1.00 93.80 4 A 1 ATOM 22 C CA . PRO A 1 4 ? -6.746 4.471 0.698 1.00 95.38 4 A 1 ATOM 23 C C . PRO A 1 4 ? -5.934 3.321 1.289 1.00 96.44 4 A 1 ATOM 24 O O . PRO A 1 4 ? -5.022 2.804 0.650 1.00 95.38 4 A 1 ATOM 25 C CB . PRO A 1 4 ? -8.102 3.977 0.195 1.00 93.61 4 A 1 ATOM 26 C CG . PRO A 1 4 ? -7.842 3.590 -1.219 1.00 91.09 4 A 1 ATOM 27 C CD . PRO A 1 4 ? -6.780 4.549 -1.725 1.00 92.37 4 A 1 ATOM 28 N N . SER A 1 5 ? -6.263 2.906 2.503 1.00 94.33 5 A 1 ATOM 29 C CA . SER A 1 5 ? -5.561 1.813 3.171 1.00 95.79 5 A 1 ATOM 30 C C . SER A 1 5 ? -5.762 0.487 2.444 1.00 96.59 5 A 1 ATOM 31 O O . SER A 1 5 ? -5.043 -0.479 2.688 1.00 95.46 5 A 1 ATOM 32 C CB . SER A 1 5 ? -6.048 1.685 4.613 1.00 94.07 5 A 1 ATOM 33 O OG . SER A 1 5 ? -7.440 1.538 4.637 1.00 87.42 5 A 1 ATOM 34 N N . VAL A 1 6 ? -6.734 0.452 1.548 1.00 96.03 6 A 1 ATOM 35 C CA . VAL A 1 6 ? -7.033 -0.756 0.784 1.00 96.23 6 A 1 ATOM 36 C C . VAL A 1 6 ? -5.899 -1.081 -0.184 1.00 96.85 6 A 1 ATOM 37 O O . VAL A 1 6 ? -5.590 -2.249 -0.429 1.00 96.01 6 A 1 ATOM 38 C CB . VAL A 1 6 ? -8.348 -0.597 0.002 1.00 95.11 6 A 1 ATOM 39 C CG1 . VAL A 1 6 ? -8.641 -1.848 -0.811 1.00 91.47 6 A 1 ATOM 40 C CG2 . VAL A 1 6 ? -9.499 -0.299 0.950 1.00 90.45 6 A 1 ATOM 41 N N . MET A 1 7 ? -5.278 -0.050 -0.739 1.00 96.06 7 A 1 ATOM 42 C CA . MET A 1 7 ? -4.184 -0.217 -1.687 1.00 96.03 7 A 1 ATOM 43 C C . MET A 1 7 ? -2.828 -0.173 -0.995 1.00 96.64 7 A 1 ATOM 44 O O . MET A 1 7 ? -1.887 -0.842 -1.409 1.00 95.82 7 A 1 ATOM 45 C CB . MET A 1 7 ? -4.254 0.875 -2.753 1.00 94.96 7 A 1 ATOM 46 C CG . MET A 1 7 ? -5.471 0.752 -3.651 1.00 90.96 7 A 1 ATOM 47 S SD . MET A 1 7 ? -5.280 -0.526 -4.883 1.00 87.34 7 A 1 ATOM 48 C CE . MET A 1 7 ? -6.725 -0.210 -5.896 1.00 81.18 7 A 1 ATOM 49 N N . VAL A 1 8 ? -2.737 0.616 0.031 1.00 97.06 8 A 1 ATOM 50 C CA . VAL A 1 8 ? -1.486 0.799 0.756 1.00 97.10 8 A 1 ATOM 51 C C . VAL A 1 8 ? -1.060 -0.459 1.504 1.00 97.45 8 A 1 ATOM 52 O O . VAL A 1 8 ? 0.093 -0.871 1.429 1.00 97.04 8 A 1 ATOM 53 C CB . VAL A 1 8 ? -1.594 1.970 1.744 1.00 96.49 8 A 1 ATOM 54 C CG1 . VAL A 1 8 ? -0.293 2.130 2.515 1.00 94.27 8 A 1 ATOM 55 C CG2 . VAL A 1 8 ? -1.934 3.252 1.007 1.00 93.58 8 A 1 ATOM 56 N N . LEU A 1 9 ? -1.978 -1.052 2.230 1.00 96.62 9 A 1 ATOM 57 C CA . LEU A 1 9 ? -1.670 -2.231 3.038 1.00 96.41 9 A 1 ATOM 58 C C . LEU A 1 9 ? -1.082 -3.384 2.216 1.00 96.87 9 A 1 ATOM 59 O O . LEU A 1 9 ? 0.019 -3.853 2.519 1.00 96.44 9 A 1 ATOM 60 C CB . LEU A 1 9 ? -2.924 -2.684 3.790 1.00 95.89 9 A 1 ATOM 61 C CG . LEU A 1 9 ? -2.673 -3.729 4.865 1.00 93.25 9 A 1 ATOM 62 C CD1 . LEU A 1 9 ? -1.766 -3.163 5.952 1.00 91.78 9 A 1 ATOM 63 C CD2 . LEU A 1 9 ? -3.990 -4.192 5.464 1.00 91.38 9 A 1 ATOM 64 N N . PRO A 1 10 ? -1.784 -3.854 1.183 1.00 97.25 10 A 1 ATOM 65 C CA . PRO A 1 10 ? -1.278 -4.959 0.363 1.00 97.33 10 A 1 ATOM 66 C C . PRO A 1 10 ? -0.066 -4.572 -0.463 1.00 97.69 10 A 1 ATOM 67 O O . PRO A 1 10 ? 0.887 -5.349 -0.575 1.00 97.08 10 A 1 ATOM 68 C CB . PRO A 1 10 ? -2.466 -5.307 -0.539 1.00 96.71 10 A 1 ATOM 69 C CG . PRO A 1 10 ? -3.257 -4.052 -0.618 1.00 96.25 10 A 1 ATOM 70 C CD . PRO A 1 10 ? -3.082 -3.363 0.711 1.00 97.05 10 A 1 ATOM 71 N N . LEU A 1 11 ? -0.076 -3.394 -1.038 1.00 97.15 11 A 1 ATOM 72 C CA . LEU A 1 11 ? 1.031 -2.915 -1.857 1.00 96.89 11 A 1 ATOM 73 C C . LEU A 1 11 ? 2.296 -2.738 -1.027 1.00 97.34 11 A 1 ATOM 74 O O . LEU A 1 11 ? 3.392 -3.046 -1.478 1.00 96.67 11 A 1 ATOM 75 C CB . LEU A 1 11 ? 0.662 -1.587 -2.527 1.00 96.31 11 A 1 ATOM 76 C CG . LEU A 1 11 ? 0.666 -1.650 -4.050 1.00 93.31 11 A 1 ATOM 77 C CD1 . LEU A 1 11 ? -0.642 -2.229 -4.563 1.00 91.97 11 A 1 ATOM 78 C CD2 . LEU A 1 11 ? 0.899 -0.271 -4.636 1.00 92.17 11 A 1 ATOM 79 N N . LEU A 1 12 ? 2.141 -2.246 0.183 1.00 96.75 12 A 1 ATOM 80 C CA . LEU A 1 12 ? 3.272 -2.010 1.074 1.00 96.66 12 A 1 ATOM 81 C C . LEU A 1 12 ? 4.037 -3.305 1.325 1.00 97.32 12 A 1 ATOM 82 O O . LEU A 1 12 ? 5.263 -3.342 1.265 1.00 97.06 12 A 1 ATOM 83 C CB . LEU A 1 12 ? 2.782 -1.430 2.401 1.00 96.13 12 A 1 ATOM 84 C CG . LEU A 1 12 ? 3.688 -0.337 2.960 1.00 93.98 12 A 1 ATOM 85 C CD1 . LEU A 1 12 ? 3.433 0.984 2.238 1.00 92.73 12 A 1 ATOM 86 C CD2 . LEU A 1 12 ? 3.462 -0.169 4.453 1.00 92.74 12 A 1 ATOM 87 N N . ILE A 1 13 ? 3.317 -4.366 1.597 1.00 97.52 13 A 1 ATOM 88 C CA . ILE A 1 13 ? 3.929 -5.656 1.877 1.00 97.50 13 A 1 ATOM 89 C C . ILE A 1 13 ? 4.616 -6.216 0.636 1.00 97.85 13 A 1 ATOM 90 O O . ILE A 1 13 ? 5.707 -6.779 0.720 1.00 97.38 13 A 1 ATOM 91 C CB . ILE A 1 13 ? 2.876 -6.649 2.383 1.00 97.23 13 A 1 ATOM 92 C CG1 . ILE A 1 13 ? 2.263 -6.146 3.690 1.00 96.42 13 A 1 ATOM 93 C CG2 . ILE A 1 13 ? 3.514 -8.020 2.605 1.00 96.09 13 A 1 ATOM 94 C CD1 . ILE A 1 13 ? 0.997 -6.874 4.065 1.00 94.29 13 A 1 ATOM 95 N N . VAL A 1 14 ? 3.995 -6.063 -0.508 1.00 97.94 14 A 1 ATOM 96 C CA . VAL A 1 14 ? 4.547 -6.556 -1.766 1.00 97.85 14 A 1 ATOM 97 C C . VAL A 1 14 ? 5.806 -5.797 -2.155 1.00 98.06 14 A 1 ATOM 98 O O . VAL A 1 14 ? 6.788 -6.394 -2.607 1.00 97.62 14 A 1 ATOM 99 C CB . VAL A 1 14 ? 3.514 -6.443 -2.896 1.00 97.41 14 A 1 ATOM 100 C CG1 . VAL A 1 14 ? 4.126 -6.859 -4.228 1.00 96.07 14 A 1 ATOM 101 C CG2 . VAL A 1 14 ? 2.295 -7.293 -2.592 1.00 95.79 14 A 1 ATOM 102 N N . VAL A 1 15 ? 5.781 -4.494 -1.991 1.00 97.87 15 A 1 ATOM 103 C CA . VAL A 1 15 ? 6.917 -3.646 -2.345 1.00 97.70 15 A 1 ATOM 104 C C . VAL A 1 15 ? 8.081 -3.843 -1.380 1.00 97.94 15 A 1 ATOM 105 O O . VAL A 1 15 ? 9.241 -3.920 -1.792 1.00 97.47 15 A 1 ATOM 106 C CB . VAL A 1 15 ? 6.509 -2.158 -2.366 1.00 97.10 15 A 1 ATOM 107 C CG1 . VAL A 1 15 ? 7.726 -1.269 -2.600 1.00 95.00 15 A 1 ATOM 108 C CG2 . VAL A 1 15 ? 5.473 -1.904 -3.451 1.00 94.56 15 A 1 ATOM 109 N N . PHE A 1 16 ? 7.788 -3.908 -0.097 1.00 97.64 16 A 1 ATOM 110 C CA . PHE A 1 16 ? 8.818 -4.051 0.924 1.00 97.46 16 A 1 ATOM 111 C C . PHE A 1 16 ? 9.295 -5.494 1.047 1.00 97.71 16 A 1 ATOM 112 O O . PHE A 1 16 ? 10.466 -5.745 1.325 1.00 97.10 16 A 1 ATOM 113 C CB . PHE A 1 16 ? 8.297 -3.552 2.271 1.00 96.82 16 A 1 ATOM 114 C CG . PHE A 1 16 ? 8.307 -2.041 2.382 1.00 95.19 16 A 1 ATOM 115 C CD1 . PHE A 1 16 ? 7.310 -1.277 1.797 1.00 92.63 16 A 1 ATOM 116 C CD2 . PHE A 1 16 ? 9.324 -1.397 3.070 1.00 92.72 16 A 1 ATOM 117 C CE1 . PHE A 1 16 ? 7.325 0.110 1.888 1.00 92.55 16 A 1 ATOM 118 C CE2 . PHE A 1 16 ? 9.345 -0.009 3.169 1.00 92.00 16 A 1 ATOM 119 C CZ . PHE A 1 16 ? 8.343 0.748 2.577 1.00 92.58 16 A 1 ATOM 120 N N . ALA A 1 17 ? 8.411 -6.433 0.852 1.00 97.08 17 A 1 ATOM 121 C CA . ALA A 1 17 ? 8.732 -7.858 0.955 1.00 96.24 17 A 1 ATOM 122 C C . ALA A 1 17 ? 9.008 -8.440 -0.421 1.00 95.08 17 A 1 ATOM 123 O O . ALA A 1 17 ? 10.131 -8.938 -0.648 1.00 92.84 17 A 1 ATOM 124 C CB . ALA A 1 17 ? 7.585 -8.600 1.637 1.00 93.94 17 A 1 ATOM 125 O OXT . ALA A 1 17 ? 8.101 -8.386 -1.258 1.00 86.42 17 A 1 #