# 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_spkb38238 # _entry.id spkb38238 # 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" "C5 H10 N2 O3" 146.144 GLN y GLUTAMINE C(CC(=O)N)[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" "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" "C9 H11 N O2" 165.189 PHE y PHENYLALANINE c1ccc(cc1)C[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" "C4 H9 N O3" 119.119 THR y THREONINE C[C@H]([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 LYS 2 1 n GLN 3 1 n THR 4 1 n VAL 5 1 n LEU 6 1 n LEU 7 1 n LEU 8 1 n PHE 9 1 n THR 10 1 n ALA 11 1 n LEU 12 1 n PHE 13 1 n LEU 14 1 n SER 15 1 n GLY 16 # _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 @ 2025-07-10 12:55:54)" _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 91.60 1 1 A LYS 2 2 92.23 1 2 A GLN 3 2 92.23 1 3 A THR 4 2 97.13 1 4 A VAL 5 2 98.04 1 5 A LEU 6 2 96.97 1 6 A LEU 7 2 97.05 1 7 A LEU 8 2 96.70 1 8 A PHE 9 2 96.58 1 9 A THR 10 2 97.42 1 10 A ALA 11 2 98.58 1 11 A LEU 12 2 96.71 1 12 A PHE 13 2 96.20 1 13 A LEU 14 2 96.37 1 14 A SER 15 2 96.27 1 15 A GLY 16 2 90.40 1 16 # _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 LYS . 2 A 2 A 3 1 n GLN . 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 PHE . 9 A 9 A 10 1 n THR . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n PHE . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n SER . 15 A 15 A 16 1 n GLY . 16 A 16 # _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 ? -8.121 -5.788 5.070 1.00 96.61 1 A 1 ATOM 2 C CA . MET A 1 1 ? -7.918 -4.565 5.865 1.00 97.11 1 A 1 ATOM 3 C C . MET A 1 1 ? -7.580 -3.387 4.955 1.00 97.18 1 A 1 ATOM 4 O O . MET A 1 1 ? -6.669 -3.480 4.138 1.00 95.95 1 A 1 ATOM 5 C CB . MET A 1 1 ? -6.779 -4.745 6.871 1.00 94.79 1 A 1 ATOM 6 C CG . MET A 1 1 ? -6.938 -5.973 7.752 1.00 89.43 1 A 1 ATOM 7 S SD . MET A 1 1 ? -5.556 -6.179 8.887 1.00 85.75 1 A 1 ATOM 8 C CE . MET A 1 1 ? -5.866 -7.831 9.466 1.00 76.01 1 A 1 ATOM 9 N N . LYS A 1 2 ? -8.293 -2.297 5.103 1.00 97.58 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -8.045 -1.100 4.302 1.00 97.94 2 A 1 ATOM 11 C C . LYS A 1 2 ? -6.757 -0.401 4.732 1.00 98.09 2 A 1 ATOM 12 O O . LYS A 1 2 ? -6.124 0.301 3.943 1.00 97.75 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -9.233 -0.142 4.410 1.00 97.18 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -9.473 0.377 5.817 1.00 92.14 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -10.648 1.341 5.851 1.00 89.64 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -10.869 1.889 7.246 1.00 82.86 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -12.021 2.829 7.282 1.00 76.91 2 A 1 ATOM 18 N N . GLN A 1 3 ? -6.379 -0.592 5.991 1.00 97.48 3 A 1 ATOM 19 C CA . GLN A 1 3 ? -5.174 0.022 6.542 1.00 98.13 3 A 1 ATOM 20 C C . GLN A 1 3 ? -3.925 -0.508 5.847 1.00 98.44 3 A 1 ATOM 21 O O . GLN A 1 3 ? -2.999 0.247 5.540 1.00 97.62 3 A 1 ATOM 22 C CB . GLN A 1 3 ? -5.087 -0.260 8.044 1.00 97.42 3 A 1 ATOM 23 C CG . GLN A 1 3 ? -6.225 0.349 8.838 1.00 92.36 3 A 1 ATOM 24 C CD . GLN A 1 3 ? -6.184 -0.071 10.291 1.00 88.66 3 A 1 ATOM 25 O OE1 . GLN A 1 3 ? -6.516 -1.193 10.630 1.00 81.89 3 A 1 ATOM 26 N NE2 . GLN A 1 3 ? -5.756 0.818 11.162 1.00 78.08 3 A 1 ATOM 27 N N . THR A 1 4 ? -3.901 -1.796 5.594 1.00 98.25 4 A 1 ATOM 28 C CA . THR A 1 4 ? -2.761 -2.431 4.940 1.00 98.45 4 A 1 ATOM 29 C C . THR A 1 4 ? -2.535 -1.850 3.550 1.00 98.58 4 A 1 ATOM 30 O O . THR A 1 4 ? -1.397 -1.608 3.149 1.00 98.34 4 A 1 ATOM 31 C CB . THR A 1 4 ? -2.971 -3.945 4.829 1.00 98.28 4 A 1 ATOM 32 O OG1 . THR A 1 4 ? -3.313 -4.474 6.108 1.00 95.02 4 A 1 ATOM 33 C CG2 . THR A 1 4 ? -1.716 -4.624 4.322 1.00 92.99 4 A 1 ATOM 34 N N . VAL A 1 5 ? -3.608 -1.615 2.833 1.00 98.65 5 A 1 ATOM 35 C CA . VAL A 1 5 ? -3.521 -1.060 1.489 1.00 98.68 5 A 1 ATOM 36 C C . VAL A 1 5 ? -2.909 0.337 1.513 1.00 98.72 5 A 1 ATOM 37 O O . VAL A 1 5 ? -2.005 0.645 0.732 1.00 98.58 5 A 1 ATOM 38 C CB . VAL A 1 5 ? -4.904 -1.006 0.831 1.00 98.53 5 A 1 ATOM 39 C CG1 . VAL A 1 5 ? -4.810 -0.407 -0.559 1.00 96.86 5 A 1 ATOM 40 C CG2 . VAL A 1 5 ? -5.504 -2.399 0.767 1.00 96.24 5 A 1 ATOM 41 N N . LEU A 1 6 ? -3.387 1.157 2.417 1.00 98.72 6 A 1 ATOM 42 C CA . LEU A 1 6 ? -2.889 2.523 2.539 1.00 98.71 6 A 1 ATOM 43 C C . LEU A 1 6 ? -1.431 2.553 2.982 1.00 98.72 6 A 1 ATOM 44 O O . LEU A 1 6 ? -0.617 3.295 2.430 1.00 98.64 6 A 1 ATOM 45 C CB . LEU A 1 6 ? -3.750 3.306 3.529 1.00 98.61 6 A 1 ATOM 46 C CG . LEU A 1 6 ? -3.348 4.770 3.686 1.00 95.86 6 A 1 ATOM 47 C CD1 . LEU A 1 6 ? -3.483 5.510 2.365 1.00 92.39 6 A 1 ATOM 48 C CD2 . LEU A 1 6 ? -4.204 5.435 4.752 1.00 94.11 6 A 1 ATOM 49 N N . LEU A 1 7 ? -1.098 1.751 3.983 1.00 98.70 7 A 1 ATOM 50 C CA . LEU A 1 7 ? 0.262 1.705 4.511 1.00 98.65 7 A 1 ATOM 51 C C . LEU A 1 7 ? 1.242 1.176 3.471 1.00 98.66 7 A 1 ATOM 52 O O . LEU A 1 7 ? 2.341 1.711 3.312 1.00 98.58 7 A 1 ATOM 53 C CB . LEU A 1 7 ? 0.309 0.823 5.762 1.00 98.57 7 A 1 ATOM 54 C CG . LEU A 1 7 ? -0.418 1.410 6.973 1.00 96.21 7 A 1 ATOM 55 C CD1 . LEU A 1 7 ? -0.471 0.390 8.102 1.00 92.71 7 A 1 ATOM 56 C CD2 . LEU A 1 7 ? 0.273 2.675 7.456 1.00 94.35 7 A 1 ATOM 57 N N . LEU A 1 8 ? 0.844 0.137 2.766 1.00 98.54 8 A 1 ATOM 58 C CA . LEU A 1 8 ? 1.696 -0.453 1.741 1.00 98.51 8 A 1 ATOM 59 C C . LEU A 1 8 ? 1.922 0.529 0.601 1.00 98.54 8 A 1 ATOM 60 O O . LEU A 1 8 ? 3.050 0.694 0.126 1.00 98.48 8 A 1 ATOM 61 C CB . LEU A 1 8 ? 1.059 -1.738 1.213 1.00 98.47 8 A 1 ATOM 62 C CG . LEU A 1 8 ? 1.880 -2.460 0.149 1.00 95.73 8 A 1 ATOM 63 C CD1 . LEU A 1 8 ? 3.239 -2.865 0.700 1.00 91.63 8 A 1 ATOM 64 C CD2 . LEU A 1 8 ? 1.128 -3.683 -0.348 1.00 93.68 8 A 1 ATOM 65 N N . PHE A 1 9 ? 0.858 1.174 0.169 1.00 98.54 9 A 1 ATOM 66 C CA . PHE A 1 9 ? 0.943 2.156 -0.903 1.00 98.47 9 A 1 ATOM 67 C C . PHE A 1 9 ? 1.849 3.314 -0.502 1.00 98.51 9 A 1 ATOM 68 O O . PHE A 1 9 ? 2.697 3.749 -1.284 1.00 98.36 9 A 1 ATOM 69 C CB . PHE A 1 9 ? -0.453 2.674 -1.241 1.00 98.30 9 A 1 ATOM 70 C CG . PHE A 1 9 ? -0.454 3.638 -2.396 1.00 97.20 9 A 1 ATOM 71 C CD1 . PHE A 1 9 ? -0.370 5.006 -2.175 1.00 93.78 9 A 1 ATOM 72 C CD2 . PHE A 1 9 ? -0.522 3.168 -3.697 1.00 94.97 9 A 1 ATOM 73 C CE1 . PHE A 1 9 ? -0.354 5.897 -3.237 1.00 94.53 9 A 1 ATOM 74 C CE2 . PHE A 1 9 ? -0.504 4.058 -4.765 1.00 94.62 9 A 1 ATOM 75 C CZ . PHE A 1 9 ? -0.421 5.421 -4.534 1.00 95.12 9 A 1 ATOM 76 N N . THR A 1 10 ? 1.679 3.796 0.715 1.00 98.55 10 A 1 ATOM 77 C CA . THR A 1 10 ? 2.488 4.902 1.221 1.00 98.48 10 A 1 ATOM 78 C C . THR A 1 10 ? 3.959 4.505 1.300 1.00 98.54 10 A 1 ATOM 79 O O . THR A 1 10 ? 4.840 5.285 0.944 1.00 98.24 10 A 1 ATOM 80 C CB . THR A 1 10 ? 2.007 5.329 2.611 1.00 98.19 10 A 1 ATOM 81 O OG1 . THR A 1 10 ? 0.636 5.697 2.558 1.00 95.34 10 A 1 ATOM 82 C CG2 . THR A 1 10 ? 2.812 6.516 3.114 1.00 94.59 10 A 1 ATOM 83 N N . ALA A 1 11 ? 4.228 3.293 1.771 1.00 98.70 11 A 1 ATOM 84 C CA . ALA A 1 11 ? 5.599 2.803 1.883 1.00 98.65 11 A 1 ATOM 85 C C . ALA A 1 11 ? 6.279 2.773 0.519 1.00 98.68 11 A 1 ATOM 86 O O . ALA A 1 11 ? 7.430 3.184 0.384 1.00 98.37 11 A 1 ATOM 87 C CB . ALA A 1 11 ? 5.607 1.411 2.501 1.00 98.48 11 A 1 ATOM 88 N N . LEU A 1 12 ? 5.568 2.283 -0.483 1.00 98.64 12 A 1 ATOM 89 C CA . LEU A 1 12 ? 6.100 2.221 -1.839 1.00 98.54 12 A 1 ATOM 90 C C . LEU A 1 12 ? 6.339 3.617 -2.395 1.00 98.53 12 A 1 ATOM 91 O O . LEU A 1 12 ? 7.367 3.877 -3.027 1.00 98.12 12 A 1 ATOM 92 C CB . LEU A 1 12 ? 5.131 1.458 -2.739 1.00 98.30 12 A 1 ATOM 93 C CG . LEU A 1 12 ? 5.607 1.300 -4.181 1.00 96.28 12 A 1 ATOM 94 C CD1 . LEU A 1 12 ? 6.896 0.505 -4.235 1.00 92.25 12 A 1 ATOM 95 C CD2 . LEU A 1 12 ? 4.528 0.625 -5.008 1.00 92.98 12 A 1 ATOM 96 N N . PHE A 1 13 ? 5.397 4.509 -2.156 1.00 98.51 13 A 1 ATOM 97 C CA . PHE A 1 13 ? 5.496 5.883 -2.629 1.00 98.37 13 A 1 ATOM 98 C C . PHE A 1 13 ? 6.670 6.610 -1.987 1.00 98.44 13 A 1 ATOM 99 O O . PHE A 1 13 ? 7.396 7.347 -2.654 1.00 98.09 13 A 1 ATOM 100 C CB . PHE A 1 13 ? 4.191 6.625 -2.332 1.00 98.07 13 A 1 ATOM 101 C CG . PHE A 1 13 ? 4.127 7.977 -2.983 1.00 96.77 13 A 1 ATOM 102 C CD1 . PHE A 1 13 ? 4.531 9.112 -2.300 1.00 93.57 13 A 1 ATOM 103 C CD2 . PHE A 1 13 ? 3.679 8.099 -4.288 1.00 94.29 13 A 1 ATOM 104 C CE1 . PHE A 1 13 ? 4.483 10.359 -2.908 1.00 93.68 13 A 1 ATOM 105 C CE2 . PHE A 1 13 ? 3.633 9.345 -4.901 1.00 94.01 13 A 1 ATOM 106 C CZ . PHE A 1 13 ? 4.035 10.473 -4.210 1.00 94.43 13 A 1 ATOM 107 N N . LEU A 1 14 ? 6.873 6.395 -0.695 1.00 98.42 14 A 1 ATOM 108 C CA . LEU A 1 14 ? 7.965 7.032 0.032 1.00 98.25 14 A 1 ATOM 109 C C . LEU A 1 14 ? 9.317 6.480 -0.391 1.00 98.30 14 A 1 ATOM 110 O O . LEU A 1 14 ? 10.337 7.169 -0.290 1.00 97.77 14 A 1 ATOM 111 C CB . LEU A 1 14 ? 7.774 6.829 1.536 1.00 97.86 14 A 1 ATOM 112 C CG . LEU A 1 14 ? 6.596 7.600 2.125 1.00 95.72 14 A 1 ATOM 113 C CD1 . LEU A 1 14 ? 6.380 7.196 3.570 1.00 92.42 14 A 1 ATOM 114 C CD2 . LEU A 1 14 ? 6.833 9.095 2.020 1.00 92.25 14 A 1 ATOM 115 N N . SER A 1 15 ? 9.344 5.238 -0.851 1.00 98.26 15 A 1 ATOM 116 C CA . SER A 1 15 ? 10.579 4.605 -1.300 1.00 98.07 15 A 1 ATOM 117 C C . SER A 1 15 ? 11.110 5.258 -2.571 1.00 97.78 15 A 1 ATOM 118 O O . SER A 1 15 ? 12.300 5.156 -2.880 1.00 95.38 15 A 1 ATOM 119 C CB . SER A 1 15 ? 10.356 3.112 -1.539 1.00 97.08 15 A 1 ATOM 120 O OG . SER A 1 15 ? 9.973 2.466 -0.339 1.00 91.04 15 A 1 ATOM 121 N N . GLY A 1 16 ? 10.246 5.913 -3.301 1.00 95.31 16 A 1 ATOM 122 C CA . GLY A 1 16 ? 10.625 6.601 -4.531 1.00 92.69 16 A 1 ATOM 123 C C . GLY A 1 16 ? 10.763 8.080 -4.319 1.00 89.48 16 A 1 ATOM 124 O O . GLY A 1 16 ? 11.815 8.524 -3.832 1.00 85.55 16 A 1 ATOM 125 O OXT . GLY A 1 16 ? 9.806 8.803 -4.639 1.00 88.96 16 A 1 #