# 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_spkb36416 # _entry.id spkb36416 # 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" "C3 H7 N O2 S" 121.158 CYS y CYSTEINE C([C@@H](C(=O)O)N)S ? "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" "C6 H15 N2 O2" 147.195 LYS y LYSINE C(CC[NH3+])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" "C4 H9 N O3" 119.119 THR y THREONINE C[C@H]([C@@H](C(=O)O)N)O ? "L-PEPTIDE LINKING" "C9 H11 N O3" 181.189 TYR y TYROSINE c1cc(ccc1C[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 MET 2 1 n LYS 3 1 n THR 4 1 n VAL 5 1 n LEU 6 1 n LEU 7 1 n LEU 8 1 n VAL 9 1 n VAL 10 1 n LEU 11 1 n VAL 12 1 n GLY 13 1 n VAL 14 1 n ALA 15 1 n TYR 16 1 n CYS 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 @ 2025-07-02 14:35:21)" _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 95.64 _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 89.76 1 1 A MET 2 2 92.26 1 2 A LYS 3 2 91.85 1 3 A THR 4 2 97.00 1 4 A VAL 5 2 97.80 1 5 A LEU 6 2 96.25 1 6 A LEU 7 2 96.43 1 7 A LEU 8 2 96.91 1 8 A VAL 9 2 98.27 1 9 A VAL 10 2 98.43 1 10 A LEU 11 2 97.23 1 11 A VAL 12 2 98.14 1 12 A GLY 13 2 98.41 1 13 A VAL 14 2 97.95 1 14 A ALA 15 2 98.29 1 15 A TYR 16 2 94.34 1 16 A CYS 17 2 91.24 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 MET . 2 A 2 A 3 1 n LYS . 3 A 3 A 4 1 n THR . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n VAL . 9 A 9 A 10 1 n VAL . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n VAL . 12 A 12 A 13 1 n GLY . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n TYR . 16 A 16 A 17 1 n CYS . 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 ? -8.622 7.227 9.213 1.00 95.61 1 A 1 ATOM 2 C CA . MET A 1 1 ? -7.252 7.760 9.146 1.00 96.36 1 A 1 ATOM 3 C C . MET A 1 1 ? -6.695 7.628 7.731 1.00 96.90 1 A 1 ATOM 4 O O . MET A 1 1 ? -6.147 6.589 7.371 1.00 95.39 1 A 1 ATOM 5 C CB . MET A 1 1 ? -6.334 7.019 10.115 1.00 92.64 1 A 1 ATOM 6 C CG . MET A 1 1 ? -6.724 7.211 11.568 1.00 84.36 1 A 1 ATOM 7 S SD . MET A 1 1 ? -5.655 6.305 12.691 1.00 82.12 1 A 1 ATOM 8 C CE . MET A 1 1 ? -6.338 6.796 14.257 1.00 74.70 1 A 1 ATOM 9 N N . MET A 1 2 ? -6.849 8.680 6.926 1.00 97.31 2 A 1 ATOM 10 C CA . MET A 1 2 ? -6.376 8.661 5.541 1.00 97.56 2 A 1 ATOM 11 C C . MET A 1 2 ? -4.856 8.525 5.465 1.00 97.83 2 A 1 ATOM 12 O O . MET A 1 2 ? -4.327 7.886 4.557 1.00 97.13 2 A 1 ATOM 13 C CB . MET A 1 2 ? -6.817 9.935 4.821 1.00 96.24 2 A 1 ATOM 14 C CG . MET A 1 2 ? -8.318 10.054 4.689 1.00 90.71 2 A 1 ATOM 15 S SD . MET A 1 2 ? -8.832 11.422 3.647 1.00 86.12 2 A 1 ATOM 16 C CE . MET A 1 2 ? -8.169 12.809 4.550 1.00 75.22 2 A 1 ATOM 17 N N . LYS A 1 3 ? -4.158 9.126 6.427 1.00 97.60 3 A 1 ATOM 18 C CA . LYS A 1 3 ? -2.697 9.051 6.491 1.00 97.98 3 A 1 ATOM 19 C C . LYS A 1 3 ? -2.231 7.604 6.639 1.00 98.32 3 A 1 ATOM 20 O O . LYS A 1 3 ? -1.288 7.176 5.974 1.00 98.12 3 A 1 ATOM 21 C CB . LYS A 1 3 ? -2.182 9.881 7.673 1.00 97.40 3 A 1 ATOM 22 C CG . LYS A 1 3 ? -2.538 11.359 7.607 1.00 92.16 3 A 1 ATOM 23 C CD . LYS A 1 3 ? -1.780 12.082 6.532 1.00 88.76 3 A 1 ATOM 24 C CE . LYS A 1 3 ? -2.059 13.577 6.565 1.00 81.54 3 A 1 ATOM 25 N NZ . LYS A 1 3 ? -1.559 14.205 7.820 1.00 74.80 3 A 1 ATOM 26 N N . THR A 1 4 ? -2.912 6.854 7.501 1.00 98.34 4 A 1 ATOM 27 C CA . THR A 1 4 ? -2.568 5.456 7.747 1.00 98.51 4 A 1 ATOM 28 C C . THR A 1 4 ? -2.795 4.611 6.499 1.00 98.64 4 A 1 ATOM 29 O O . THR A 1 4 ? -1.974 3.759 6.156 1.00 98.41 4 A 1 ATOM 30 C CB . THR A 1 4 ? -3.397 4.887 8.903 1.00 98.27 4 A 1 ATOM 31 O OG1 . THR A 1 4 ? -3.307 5.757 10.034 1.00 93.81 4 A 1 ATOM 32 C CG2 . THR A 1 4 ? -2.904 3.508 9.296 1.00 93.02 4 A 1 ATOM 33 N N . VAL A 1 5 ? -3.914 4.859 5.807 1.00 98.46 5 A 1 ATOM 34 C CA . VAL A 1 5 ? -4.235 4.140 4.578 1.00 98.55 5 A 1 ATOM 35 C C . VAL A 1 5 ? -3.184 4.423 3.510 1.00 98.60 5 A 1 ATOM 36 O O . VAL A 1 5 ? -2.735 3.517 2.804 1.00 98.42 5 A 1 ATOM 37 C CB . VAL A 1 5 ? -5.629 4.523 4.056 1.00 98.38 5 A 1 ATOM 38 C CG1 . VAL A 1 5 ? -5.927 3.823 2.738 1.00 96.18 5 A 1 ATOM 39 C CG2 . VAL A 1 5 ? -6.691 4.174 5.087 1.00 96.02 5 A 1 ATOM 40 N N . LEU A 1 6 ? -2.787 5.681 3.399 1.00 98.41 6 A 1 ATOM 41 C CA . LEU A 1 6 ? -1.771 6.084 2.432 1.00 98.40 6 A 1 ATOM 42 C C . LEU A 1 6 ? -0.453 5.366 2.694 1.00 98.55 6 A 1 ATOM 43 O O . LEU A 1 6 ? 0.184 4.868 1.761 1.00 98.57 6 A 1 ATOM 44 C CB . LEU A 1 6 ? -1.565 7.597 2.491 1.00 98.37 6 A 1 ATOM 45 C CG . LEU A 1 6 ? -0.558 8.138 1.477 1.00 93.81 6 A 1 ATOM 46 C CD1 . LEU A 1 6 ? -1.021 7.877 0.052 1.00 91.09 6 A 1 ATOM 47 C CD2 . LEU A 1 6 ? -0.339 9.628 1.698 1.00 92.84 6 A 1 ATOM 48 N N . LEU A 1 7 ? -0.058 5.305 3.958 1.00 98.51 7 A 1 ATOM 49 C CA . LEU A 1 7 ? 1.178 4.629 4.345 1.00 98.53 7 A 1 ATOM 50 C C . LEU A 1 7 ? 1.130 3.149 3.982 1.00 98.65 7 A 1 ATOM 51 O O . LEU A 1 7 ? 2.119 2.587 3.507 1.00 98.63 7 A 1 ATOM 52 C CB . LEU A 1 7 ? 1.412 4.785 5.850 1.00 98.47 7 A 1 ATOM 53 C CG . LEU A 1 7 ? 1.798 6.196 6.292 1.00 93.90 7 A 1 ATOM 54 C CD1 . LEU A 1 7 ? 1.797 6.291 7.812 1.00 91.61 7 A 1 ATOM 55 C CD2 . LEU A 1 7 ? 3.165 6.580 5.748 1.00 93.10 7 A 1 ATOM 56 N N . LEU A 1 8 ? -0.029 2.533 4.186 1.00 98.60 8 A 1 ATOM 57 C CA . LEU A 1 8 ? -0.212 1.126 3.860 1.00 98.60 8 A 1 ATOM 58 C C . LEU A 1 8 ? -0.086 0.896 2.358 1.00 98.68 8 A 1 ATOM 59 O O . LEU A 1 8 ? 0.589 -0.035 1.917 1.00 98.59 8 A 1 ATOM 60 C CB . LEU A 1 8 ? -1.577 0.655 4.354 1.00 98.51 8 A 1 ATOM 61 C CG . LEU A 1 8 ? -1.861 -0.829 4.121 1.00 95.81 8 A 1 ATOM 62 C CD1 . LEU A 1 8 ? -0.876 -1.700 4.887 1.00 92.74 8 A 1 ATOM 63 C CD2 . LEU A 1 8 ? -3.288 -1.161 4.533 1.00 93.74 8 A 1 ATOM 64 N N . VAL A 1 9 ? -0.733 1.755 1.560 1.00 98.67 9 A 1 ATOM 65 C CA . VAL A 1 9 ? -0.684 1.654 0.104 1.00 98.64 9 A 1 ATOM 66 C C . VAL A 1 9 ? 0.744 1.816 -0.402 1.00 98.69 9 A 1 ATOM 67 O O . VAL A 1 9 ? 1.190 1.077 -1.286 1.00 98.54 9 A 1 ATOM 68 C CB . VAL A 1 9 ? -1.596 2.705 -0.551 1.00 98.49 9 A 1 ATOM 69 C CG1 . VAL A 1 9 ? -1.417 2.720 -2.065 1.00 97.46 9 A 1 ATOM 70 C CG2 . VAL A 1 9 ? -3.051 2.428 -0.204 1.00 97.38 9 A 1 ATOM 71 N N . VAL A 1 10 ? 1.462 2.778 0.159 1.00 98.75 10 A 1 ATOM 72 C CA . VAL A 1 10 ? 2.853 3.014 -0.221 1.00 98.73 10 A 1 ATOM 73 C C . VAL A 1 10 ? 3.707 1.793 0.090 1.00 98.76 10 A 1 ATOM 74 O O . VAL A 1 10 ? 4.530 1.378 -0.732 1.00 98.61 10 A 1 ATOM 75 C CB . VAL A 1 10 ? 3.419 4.253 0.497 1.00 98.59 10 A 1 ATOM 76 C CG1 . VAL A 1 10 ? 4.923 4.390 0.269 1.00 97.87 10 A 1 ATOM 77 C CG2 . VAL A 1 10 ? 2.717 5.511 0.005 1.00 97.69 10 A 1 ATOM 78 N N . LEU A 1 11 ? 3.491 1.209 1.254 1.00 98.78 11 A 1 ATOM 79 C CA . LEU A 1 11 ? 4.238 0.026 1.668 1.00 98.76 11 A 1 ATOM 80 C C . LEU A 1 11 ? 4.006 -1.127 0.702 1.00 98.78 11 A 1 ATOM 81 O O . LEU A 1 11 ? 4.949 -1.814 0.303 1.00 98.60 11 A 1 ATOM 82 C CB . LEU A 1 11 ? 3.827 -0.375 3.084 1.00 98.64 11 A 1 ATOM 83 C CG . LEU A 1 11 ? 4.606 -1.554 3.667 1.00 96.33 11 A 1 ATOM 84 C CD1 . LEU A 1 11 ? 6.085 -1.224 3.785 1.00 93.44 11 A 1 ATOM 85 C CD2 . LEU A 1 11 ? 4.043 -1.938 5.026 1.00 94.51 11 A 1 ATOM 86 N N . VAL A 1 12 ? 2.746 -1.336 0.311 1.00 98.75 12 A 1 ATOM 87 C CA . VAL A 1 12 ? 2.397 -2.377 -0.651 1.00 98.67 12 A 1 ATOM 88 C C . VAL A 1 12 ? 3.054 -2.096 -1.997 1.00 98.69 12 A 1 ATOM 89 O O . VAL A 1 12 ? 3.573 -3.004 -2.652 1.00 98.33 12 A 1 ATOM 90 C CB . VAL A 1 12 ? 0.874 -2.483 -0.814 1.00 98.38 12 A 1 ATOM 91 C CG1 . VAL A 1 12 ? 0.510 -3.470 -1.920 1.00 96.96 12 A 1 ATOM 92 C CG2 . VAL A 1 12 ? 0.230 -2.915 0.494 1.00 97.22 12 A 1 ATOM 93 N N . GLY A 1 13 ? 3.047 -0.833 -2.407 1.00 98.49 13 A 1 ATOM 94 C CA . GLY A 1 13 ? 3.679 -0.439 -3.659 1.00 98.40 13 A 1 ATOM 95 C C . GLY A 1 13 ? 5.162 -0.758 -3.675 1.00 98.53 13 A 1 ATOM 96 O O . GLY A 1 13 ? 5.694 -1.229 -4.682 1.00 98.21 13 A 1 ATOM 97 N N . VAL A 1 14 ? 5.835 -0.524 -2.557 1.00 98.71 14 A 1 ATOM 98 C CA . VAL A 1 14 ? 7.259 -0.834 -2.426 1.00 98.64 14 A 1 ATOM 99 C C . VAL A 1 14 ? 7.499 -2.333 -2.545 1.00 98.69 14 A 1 ATOM 100 O O . VAL A 1 14 ? 8.477 -2.768 -3.160 1.00 98.28 14 A 1 ATOM 101 C CB . VAL A 1 14 ? 7.815 -0.314 -1.088 1.00 98.23 14 A 1 ATOM 102 C CG1 . VAL A 1 14 ? 9.257 -0.765 -0.882 1.00 96.36 14 A 1 ATOM 103 C CG2 . VAL A 1 14 ? 7.738 1.199 -1.035 1.00 96.71 14 A 1 ATOM 104 N N . ALA A 1 15 ? 6.600 -3.127 -1.981 1.00 98.52 15 A 1 ATOM 105 C CA . ALA A 1 15 ? 6.704 -4.583 -2.055 1.00 98.49 15 A 1 ATOM 106 C C . ALA A 1 15 ? 6.583 -5.078 -3.493 1.00 98.51 15 A 1 ATOM 107 O O . ALA A 1 15 ? 7.146 -6.112 -3.856 1.00 97.84 15 A 1 ATOM 108 C CB . ALA A 1 15 ? 5.632 -5.231 -1.183 1.00 98.10 15 A 1 ATOM 109 N N . TYR A 1 16 ? 5.829 -4.334 -4.311 1.00 98.11 16 A 1 ATOM 110 C CA . TYR A 1 16 ? 5.646 -4.672 -5.718 1.00 97.89 16 A 1 ATOM 111 C C . TYR A 1 16 ? 6.746 -4.074 -6.595 1.00 97.67 16 A 1 ATOM 112 O O . TYR A 1 16 ? 6.729 -4.249 -7.812 1.00 95.90 16 A 1 ATOM 113 C CB . TYR A 1 16 ? 4.270 -4.188 -6.198 1.00 97.37 16 A 1 ATOM 114 C CG . TYR A 1 16 ? 3.155 -5.167 -5.900 1.00 94.30 16 A 1 ATOM 115 C CD1 . TYR A 1 16 ? 2.505 -5.163 -4.678 1.00 92.37 16 A 1 ATOM 116 C CD2 . TYR A 1 16 ? 2.762 -6.095 -6.859 1.00 92.16 16 A 1 ATOM 117 C CE1 . TYR A 1 16 ? 1.487 -6.061 -4.409 1.00 92.01 16 A 1 ATOM 118 C CE2 . TYR A 1 16 ? 1.741 -6.998 -6.598 1.00 91.70 16 A 1 ATOM 119 C CZ . TYR A 1 16 ? 1.108 -6.975 -5.369 1.00 92.00 16 A 1 ATOM 120 O OH . TYR A 1 16 ? 0.101 -7.866 -5.110 1.00 90.55 16 A 1 ATOM 121 N N . CYS A 1 17 ? 7.690 -3.390 -5.979 1.00 97.12 17 A 1 ATOM 122 C CA . CYS A 1 17 ? 8.776 -2.746 -6.713 1.00 95.73 17 A 1 ATOM 123 C C . CYS A 1 17 ? 9.841 -3.777 -7.112 1.00 94.59 17 A 1 ATOM 124 O O . CYS A 1 17 ? 10.269 -3.776 -8.276 1.00 90.58 17 A 1 ATOM 125 C CB . CYS A 1 17 ? 9.398 -1.627 -5.876 1.00 92.72 17 A 1 ATOM 126 S SG . CYS A 1 17 ? 10.625 -0.688 -6.797 1.00 84.81 17 A 1 ATOM 127 O OXT . CYS A 1 17 ? 10.249 -4.579 -6.242 1.00 83.16 17 A 1 #