# 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_spkb29676 # _entry.id spkb29676 # 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 "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" "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 SER 2 1 n LEU 3 1 n PRO 4 1 n SER 5 1 n ILE 6 1 n PRO 7 1 n SER 8 1 n PHE 9 1 n VAL 10 1 n LEU 11 1 n SER 12 1 n GLY 13 1 n LEU 14 1 n LEU 15 1 n LEU 16 1 n ILE 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 18:04:33)" _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 89.95 _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 73.62 1 1 A SER 2 2 78.99 1 2 A LEU 3 2 80.43 1 3 A PRO 4 2 88.43 1 4 A SER 5 2 90.09 1 5 A ILE 6 2 90.36 1 6 A PRO 7 2 94.23 1 7 A SER 8 2 93.44 1 8 A PHE 9 2 92.57 1 9 A VAL 10 2 94.51 1 10 A LEU 11 2 92.85 1 11 A SER 12 2 93.86 1 12 A GLY 13 2 95.90 1 13 A LEU 14 2 94.12 1 14 A LEU 15 2 94.64 1 15 A LEU 16 2 94.19 1 16 A ILE 17 2 89.08 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 SER . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n PRO . 4 A 4 A 5 1 n SER . 5 A 5 A 6 1 n ILE . 6 A 6 A 7 1 n PRO . 7 A 7 A 8 1 n SER . 8 A 8 A 9 1 n PHE . 9 A 9 A 10 1 n VAL . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n SER . 12 A 12 A 13 1 n GLY . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n LEU . 15 A 15 A 16 1 n LEU . 16 A 16 A 17 1 n ILE . 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 ? -0.104 -16.131 1.836 1.00 76.98 1 A 1 ATOM 2 C CA . MET A 1 1 ? 0.714 -15.477 0.797 1.00 79.27 1 A 1 ATOM 3 C C . MET A 1 1 ? -0.178 -14.946 -0.317 1.00 80.56 1 A 1 ATOM 4 O O . MET A 1 1 ? 0.302 -14.393 -1.301 1.00 78.15 1 A 1 ATOM 5 C CB . MET A 1 1 ? 1.732 -16.459 0.210 1.00 73.91 1 A 1 ATOM 6 C CG . MET A 1 1 ? 2.798 -16.845 1.241 1.00 71.88 1 A 1 ATOM 7 S SD . MET A 1 1 ? 2.116 -17.811 2.579 1.00 68.58 1 A 1 ATOM 8 C CE . MET A 1 1 ? 3.561 -18.011 3.598 1.00 59.60 1 A 1 ATOM 9 N N . SER A 1 2 ? -1.466 -15.103 -0.124 1.00 78.92 2 A 1 ATOM 10 C CA . SER A 1 2 ? -2.430 -14.584 -1.097 1.00 81.94 2 A 1 ATOM 11 C C . SER A 1 2 ? -2.729 -13.119 -0.822 1.00 84.05 2 A 1 ATOM 12 O O . SER A 1 2 ? -3.406 -12.451 -1.601 1.00 80.07 2 A 1 ATOM 13 C CB . SER A 1 2 ? -3.723 -15.396 -1.034 1.00 77.71 2 A 1 ATOM 14 O OG . SER A 1 2 ? -4.299 -15.305 0.252 1.00 71.27 2 A 1 ATOM 15 N N . LEU A 1 3 ? -2.213 -12.617 0.305 1.00 83.80 3 A 1 ATOM 16 C CA . LEU A 1 3 ? -2.418 -11.225 0.694 1.00 84.53 3 A 1 ATOM 17 C C . LEU A 1 3 ? -1.082 -10.606 1.082 1.00 87.36 3 A 1 ATOM 18 O O . LEU A 1 3 ? -0.563 -10.879 2.161 1.00 84.64 3 A 1 ATOM 19 C CB . LEU A 1 3 ? -3.423 -11.163 1.850 1.00 80.15 3 A 1 ATOM 20 C CG . LEU A 1 3 ? -4.079 -9.796 2.014 1.00 77.45 3 A 1 ATOM 21 C CD1 . LEU A 1 3 ? -5.514 -9.950 2.510 1.00 74.69 3 A 1 ATOM 22 C CD2 . LEU A 1 3 ? -3.289 -8.935 2.988 1.00 70.85 3 A 1 ATOM 23 N N . PRO A 1 4 ? -0.513 -9.754 0.224 1.00 89.23 4 A 1 ATOM 24 C CA . PRO A 1 4 ? 0.798 -9.135 0.455 1.00 90.37 4 A 1 ATOM 25 C C . PRO A 1 4 ? 0.790 -8.120 1.593 1.00 91.82 4 A 1 ATOM 26 O O . PRO A 1 4 ? 1.831 -7.566 1.938 1.00 89.63 4 A 1 ATOM 27 C CB . PRO A 1 4 ? 1.117 -8.459 -0.885 1.00 86.48 4 A 1 ATOM 28 C CG . PRO A 1 4 ? -0.215 -8.209 -1.513 1.00 84.40 4 A 1 ATOM 29 C CD . PRO A 1 4 ? -1.106 -9.344 -1.046 1.00 87.06 4 A 1 ATOM 30 N N . SER A 1 5 ? -0.370 -7.879 2.186 1.00 91.55 5 A 1 ATOM 31 C CA . SER A 1 5 ? -0.516 -6.936 3.297 1.00 92.78 5 A 1 ATOM 32 C C . SER A 1 5 ? 0.121 -5.592 2.961 1.00 93.77 5 A 1 ATOM 33 O O . SER A 1 5 ? 0.966 -5.086 3.696 1.00 91.06 5 A 1 ATOM 34 C CB . SER A 1 5 ? 0.114 -7.515 4.568 1.00 89.39 5 A 1 ATOM 35 O OG . SER A 1 5 ? 1.516 -7.609 4.447 1.00 81.97 5 A 1 ATOM 36 N N . ILE A 1 6 ? -0.272 -5.022 1.847 1.00 91.41 6 A 1 ATOM 37 C CA . ILE A 1 6 ? 0.262 -3.740 1.401 1.00 92.42 6 A 1 ATOM 38 C C . ILE A 1 6 ? -0.690 -2.620 1.804 1.00 93.46 6 A 1 ATOM 39 O O . ILE A 1 6 ? -1.880 -2.674 1.496 1.00 92.95 6 A 1 ATOM 40 C CB . ILE A 1 6 ? 0.461 -3.721 -0.121 1.00 91.35 6 A 1 ATOM 41 C CG1 . ILE A 1 6 ? 1.420 -4.835 -0.548 1.00 88.75 6 A 1 ATOM 42 C CG2 . ILE A 1 6 ? 1.012 -2.364 -0.558 1.00 87.87 6 A 1 ATOM 43 C CD1 . ILE A 1 6 ? 1.509 -5.000 -2.044 1.00 84.67 6 A 1 ATOM 44 N N . PRO A 1 7 ? -0.159 -1.598 2.499 1.00 94.93 7 A 1 ATOM 45 C CA . PRO A 1 7 ? -0.981 -0.464 2.919 1.00 94.88 7 A 1 ATOM 46 C C . PRO A 1 7 ? -1.500 0.322 1.717 1.00 95.46 7 A 1 ATOM 47 O O . PRO A 1 7 ? -0.737 0.970 1.006 1.00 94.79 7 A 1 ATOM 48 C CB . PRO A 1 7 ? -0.024 0.374 3.774 1.00 93.18 7 A 1 ATOM 49 C CG . PRO A 1 7 ? 1.350 -0.054 3.381 1.00 92.28 7 A 1 ATOM 50 C CD . PRO A 1 7 ? 1.228 -1.483 2.925 1.00 94.12 7 A 1 ATOM 51 N N . SER A 1 8 ? -2.797 0.266 1.507 1.00 95.06 8 A 1 ATOM 52 C CA . SER A 1 8 ? -3.421 0.948 0.375 1.00 95.16 8 A 1 ATOM 53 C C . SER A 1 8 ? -3.177 2.452 0.414 1.00 95.92 8 A 1 ATOM 54 O O . SER A 1 8 ? -3.115 3.103 -0.625 1.00 94.47 8 A 1 ATOM 55 C CB . SER A 1 8 ? -4.922 0.673 0.369 1.00 93.16 8 A 1 ATOM 56 O OG . SER A 1 8 ? -5.502 1.085 1.584 1.00 86.85 8 A 1 ATOM 57 N N . PHE A 1 9 ? -3.020 2.995 1.630 1.00 93.99 9 A 1 ATOM 58 C CA . PHE A 1 9 ? -2.776 4.427 1.770 1.00 94.40 9 A 1 ATOM 59 C C . PHE A 1 9 ? -1.404 4.810 1.220 1.00 95.86 9 A 1 ATOM 60 O O . PHE A 1 9 ? -1.172 5.972 0.893 1.00 95.12 9 A 1 ATOM 61 C CB . PHE A 1 9 ? -2.899 4.846 3.233 1.00 93.49 9 A 1 ATOM 62 C CG . PHE A 1 9 ? -1.989 4.067 4.156 1.00 92.52 9 A 1 ATOM 63 C CD1 . PHE A 1 9 ? -0.668 4.449 4.318 1.00 90.66 9 A 1 ATOM 64 C CD2 . PHE A 1 9 ? -2.469 2.974 4.855 1.00 90.84 9 A 1 ATOM 65 C CE1 . PHE A 1 9 ? 0.172 3.753 5.173 1.00 90.49 9 A 1 ATOM 66 C CE2 . PHE A 1 9 ? -1.626 2.268 5.714 1.00 89.93 9 A 1 ATOM 67 C CZ . PHE A 1 9 ? -0.310 2.659 5.870 1.00 90.92 9 A 1 ATOM 68 N N . VAL A 1 10 ? -0.513 3.847 1.130 1.00 95.05 10 A 1 ATOM 69 C CA . VAL A 1 10 ? 0.815 4.103 0.575 1.00 95.33 10 A 1 ATOM 70 C C . VAL A 1 10 ? 0.730 4.251 -0.937 1.00 95.85 10 A 1 ATOM 71 O O . VAL A 1 10 ? 1.311 5.165 -1.517 1.00 95.29 10 A 1 ATOM 72 C CB . VAL A 1 10 ? 1.795 2.976 0.938 1.00 94.48 10 A 1 ATOM 73 C CG1 . VAL A 1 10 ? 3.126 3.170 0.225 1.00 92.90 10 A 1 ATOM 74 C CG2 . VAL A 1 10 ? 2.006 2.944 2.440 1.00 92.70 10 A 1 ATOM 75 N N . LEU A 1 11 ? 0.001 3.345 -1.557 1.00 95.51 11 A 1 ATOM 76 C CA . LEU A 1 11 ? -0.186 3.406 -3.004 1.00 94.86 11 A 1 ATOM 77 C C . LEU A 1 11 ? -1.023 4.624 -3.369 1.00 95.39 11 A 1 ATOM 78 O O . LEU A 1 11 ? -0.757 5.303 -4.356 1.00 95.15 11 A 1 ATOM 79 C CB . LEU A 1 11 ? -0.865 2.128 -3.493 1.00 93.96 11 A 1 ATOM 80 C CG . LEU A 1 11 ? 0.038 0.898 -3.432 1.00 90.46 11 A 1 ATOM 81 C CD1 . LEU A 1 11 ? -0.762 -0.355 -3.729 1.00 88.70 11 A 1 ATOM 82 C CD2 . LEU A 1 11 ? 1.187 1.039 -4.419 1.00 88.79 11 A 1 ATOM 83 N N . SER A 1 12 ? -2.026 4.902 -2.552 1.00 95.33 12 A 1 ATOM 84 C CA . SER A 1 12 ? -2.873 6.074 -2.762 1.00 95.13 12 A 1 ATOM 85 C C . SER A 1 12 ? -2.108 7.342 -2.412 1.00 96.07 12 A 1 ATOM 86 O O . SER A 1 12 ? -2.248 8.367 -3.073 1.00 94.73 12 A 1 ATOM 87 C CB . SER A 1 12 ? -4.125 5.977 -1.903 1.00 93.38 12 A 1 ATOM 88 O OG . SER A 1 12 ? -4.909 4.870 -2.299 1.00 88.49 12 A 1 ATOM 89 N N . GLY A 1 13 ? -1.289 7.258 -1.364 1.00 95.78 13 A 1 ATOM 90 C CA . GLY A 1 13 ? -0.468 8.390 -0.953 1.00 95.67 13 A 1 ATOM 91 C C . GLY A 1 13 ? 0.472 8.821 -2.053 1.00 96.59 13 A 1 ATOM 92 O O . GLY A 1 13 ? 0.627 10.010 -2.314 1.00 95.55 13 A 1 ATOM 93 N N . LEU A 1 14 ? 1.086 7.846 -2.707 1.00 96.09 14 A 1 ATOM 94 C CA . LEU A 1 14 ? 2.009 8.138 -3.805 1.00 95.73 14 A 1 ATOM 95 C C . LEU A 1 14 ? 1.303 8.936 -4.894 1.00 96.47 14 A 1 ATOM 96 O O . LEU A 1 14 ? 1.914 9.761 -5.571 1.00 95.64 14 A 1 ATOM 97 C CB . LEU A 1 14 ? 2.569 6.828 -4.373 1.00 94.96 14 A 1 ATOM 98 C CG . LEU A 1 14 ? 3.727 7.025 -5.350 1.00 92.67 14 A 1 ATOM 99 C CD1 . LEU A 1 14 ? 4.723 5.880 -5.210 1.00 90.94 14 A 1 ATOM 100 C CD2 . LEU A 1 14 ? 3.224 7.095 -6.779 1.00 90.49 14 A 1 ATOM 101 N N . LEU A 1 15 ? 0.009 8.687 -5.048 1.00 96.49 15 A 1 ATOM 102 C CA . LEU A 1 15 ? -0.785 9.409 -6.039 1.00 96.18 15 A 1 ATOM 103 C C . LEU A 1 15 ? -1.229 10.762 -5.494 1.00 96.50 15 A 1 ATOM 104 O O . LEU A 1 15 ? -1.369 11.729 -6.242 1.00 95.80 15 A 1 ATOM 105 C CB . LEU A 1 15 ? -2.008 8.571 -6.430 1.00 95.70 15 A 1 ATOM 106 C CG . LEU A 1 15 ? -3.001 9.292 -7.340 1.00 93.78 15 A 1 ATOM 107 C CD1 . LEU A 1 15 ? -2.366 9.589 -8.690 1.00 91.56 15 A 1 ATOM 108 C CD2 . LEU A 1 15 ? -4.253 8.447 -7.531 1.00 91.09 15 A 1 ATOM 109 N N . LEU A 1 16 ? -1.449 10.822 -4.184 1.00 96.04 16 A 1 ATOM 110 C CA . LEU A 1 16 ? -1.920 12.045 -3.542 1.00 95.88 16 A 1 ATOM 111 C C . LEU A 1 16 ? -0.777 12.953 -3.103 1.00 96.15 16 A 1 ATOM 112 O O . LEU A 1 16 ? -0.976 14.153 -2.936 1.00 95.10 16 A 1 ATOM 113 C CB . LEU A 1 16 ? -2.796 11.683 -2.341 1.00 94.99 16 A 1 ATOM 114 C CG . LEU A 1 16 ? -4.087 10.950 -2.718 1.00 93.27 16 A 1 ATOM 115 C CD1 . LEU A 1 16 ? -4.775 10.406 -1.475 1.00 91.67 16 A 1 ATOM 116 C CD2 . LEU A 1 16 ? -5.022 11.892 -3.467 1.00 90.43 16 A 1 ATOM 117 N N . ILE A 1 17 ? 0.398 12.377 -2.914 1.00 94.67 17 A 1 ATOM 118 C CA . ILE A 1 17 ? 1.571 13.143 -2.471 1.00 93.39 17 A 1 ATOM 119 C C . ILE A 1 17 ? 1.902 14.259 -3.467 1.00 91.10 17 A 1 ATOM 120 O O . ILE A 1 17 ? 1.437 15.390 -3.284 1.00 90.10 17 A 1 ATOM 121 C CB . ILE A 1 17 ? 2.790 12.229 -2.283 1.00 89.79 17 A 1 ATOM 122 C CG1 . ILE A 1 17 ? 2.584 11.283 -1.110 1.00 86.79 17 A 1 ATOM 123 C CG2 . ILE A 1 17 ? 4.030 13.082 -2.030 1.00 86.05 17 A 1 ATOM 124 C CD1 . ILE A 1 17 ? 3.643 10.190 -1.034 1.00 85.59 17 A 1 ATOM 125 O OXT . ILE A 1 17 ? 2.625 14.056 -4.395 1.00 84.20 17 A 1 #