# 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_spkb12449 # _entry.id spkb12449 # 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" "C5 H11 N O2 S" 149.211 MET y METHIONINE CSCC[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" "C11 H12 N2 O2" 204.225 TRP y TRYPTOPHAN c1ccc2c(c1)c(c[nH]2)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 TRP 2 1 n LEU 3 1 n LEU 4 1 n PRO 5 1 n ALA 6 1 n LEU 7 1 n LEU 8 1 n LEU 9 1 n LEU 10 1 n CYS 11 1 n LEU 12 1 n SER 13 1 n GLY 14 1 n CYS 15 1 n LEU 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 @ 2025-07-09 22:33:37)" _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 89.42 _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 81.91 1 1 A TRP 2 2 81.81 1 2 A LEU 3 2 88.37 1 3 A LEU 4 2 89.33 1 4 A PRO 5 2 93.76 1 5 A ALA 6 2 94.57 1 6 A LEU 7 2 91.53 1 7 A LEU 8 2 92.24 1 8 A LEU 9 2 92.22 1 9 A LEU 10 2 92.93 1 10 A CYS 11 2 93.77 1 11 A LEU 12 2 92.88 1 12 A SER 13 2 92.90 1 13 A GLY 14 2 94.41 1 14 A CYS 15 2 90.90 1 15 A LEU 16 2 87.65 1 16 A SER 17 2 80.91 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 TRP . 2 A 2 A 3 1 n LEU . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n PRO . 5 A 5 A 6 1 n ALA . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n CYS . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n SER . 13 A 13 A 14 1 n GLY . 14 A 14 A 15 1 n CYS . 15 A 15 A 16 1 n LEU . 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 ? -10.371 -5.260 10.411 1.00 88.68 1 A 1 ATOM 2 C CA . MET A 1 1 ? -9.909 -3.891 10.688 1.00 89.11 1 A 1 ATOM 3 C C . MET A 1 1 ? -8.398 -3.741 10.469 1.00 89.87 1 A 1 ATOM 4 O O . MET A 1 1 ? -7.727 -3.044 11.223 1.00 86.81 1 A 1 ATOM 5 C CB . MET A 1 1 ? -10.270 -3.500 12.121 1.00 83.66 1 A 1 ATOM 6 C CG . MET A 1 1 ? -9.703 -4.463 13.157 1.00 77.96 1 A 1 ATOM 7 S SD . MET A 1 1 ? -10.341 -4.133 14.815 1.00 73.54 1 A 1 ATOM 8 C CE . MET A 1 1 ? -11.842 -5.086 14.765 1.00 65.66 1 A 1 ATOM 9 N N . TRP A 1 2 ? -7.864 -4.399 9.445 1.00 88.12 2 A 1 ATOM 10 C CA . TRP A 1 2 ? -6.434 -4.340 9.147 1.00 89.67 2 A 1 ATOM 11 C C . TRP A 1 2 ? -6.188 -4.042 7.669 1.00 91.33 2 A 1 ATOM 12 O O . TRP A 1 2 ? -5.369 -4.680 7.011 1.00 88.44 2 A 1 ATOM 13 C CB . TRP A 1 2 ? -5.762 -5.654 9.536 1.00 86.58 2 A 1 ATOM 14 C CG . TRP A 1 2 ? -4.976 -5.564 10.803 1.00 81.62 2 A 1 ATOM 15 C CD1 . TRP A 1 2 ? -5.452 -5.686 12.063 1.00 79.52 2 A 1 ATOM 16 C CD2 . TRP A 1 2 ? -3.556 -5.343 10.940 1.00 81.17 2 A 1 ATOM 17 N NE1 . TRP A 1 2 ? -4.433 -5.553 12.976 1.00 76.79 2 A 1 ATOM 18 C CE2 . TRP A 1 2 ? -3.248 -5.339 12.316 1.00 79.82 2 A 1 ATOM 19 C CE3 . TRP A 1 2 ? -2.524 -5.148 10.020 1.00 76.83 2 A 1 ATOM 20 C CZ2 . TRP A 1 2 ? -1.952 -5.150 12.788 1.00 78.00 2 A 1 ATOM 21 C CZ3 . TRP A 1 2 ? -1.236 -4.958 10.487 1.00 73.99 2 A 1 ATOM 22 C CH2 . TRP A 1 2 ? -0.954 -4.956 11.860 1.00 73.49 2 A 1 ATOM 23 N N . LEU A 1 3 ? -6.918 -3.063 7.136 1.00 91.73 3 A 1 ATOM 24 C CA . LEU A 1 3 ? -6.801 -2.689 5.729 1.00 92.71 3 A 1 ATOM 25 C C . LEU A 1 3 ? -6.241 -1.275 5.567 1.00 94.48 3 A 1 ATOM 26 O O . LEU A 1 3 ? -6.362 -0.677 4.495 1.00 92.83 3 A 1 ATOM 27 C CB . LEU A 1 3 ? -8.175 -2.776 5.053 1.00 90.44 3 A 1 ATOM 28 C CG . LEU A 1 3 ? -9.151 -3.765 5.674 1.00 85.06 3 A 1 ATOM 29 C CD1 . LEU A 1 3 ? -10.569 -3.452 5.217 1.00 80.96 3 A 1 ATOM 30 C CD2 . LEU A 1 3 ? -8.772 -5.186 5.260 1.00 78.72 3 A 1 ATOM 31 N N . LEU A 1 4 ? -5.647 -0.743 6.624 1.00 92.31 4 A 1 ATOM 32 C CA . LEU A 1 4 ? -5.084 0.607 6.599 1.00 92.99 4 A 1 ATOM 33 C C . LEU A 1 4 ? -3.578 0.600 6.319 1.00 94.73 4 A 1 ATOM 34 O O . LEU A 1 4 ? -3.118 1.256 5.383 1.00 94.38 4 A 1 ATOM 35 C CB . LEU A 1 4 ? -5.383 1.327 7.923 1.00 91.15 4 A 1 ATOM 36 C CG . LEU A 1 4 ? -6.455 2.414 7.821 1.00 86.54 4 A 1 ATOM 37 C CD1 . LEU A 1 4 ? -5.994 3.542 6.930 1.00 82.21 4 A 1 ATOM 38 C CD2 . LEU A 1 4 ? -7.757 1.810 7.306 1.00 80.32 4 A 1 ATOM 39 N N . PRO A 1 5 ? -2.792 -0.112 7.134 1.00 94.36 5 A 1 ATOM 40 C CA . PRO A 1 5 ? -1.334 -0.174 6.937 1.00 94.96 5 A 1 ATOM 41 C C . PRO A 1 5 ? -0.938 -0.890 5.655 1.00 95.78 5 A 1 ATOM 42 O O . PRO A 1 5 ? -0.009 -0.473 4.962 1.00 94.92 5 A 1 ATOM 43 C CB . PRO A 1 5 ? -0.844 -0.943 8.170 1.00 92.88 5 A 1 ATOM 44 C CG . PRO A 1 5 ? -2.015 -1.743 8.614 1.00 90.42 5 A 1 ATOM 45 C CD . PRO A 1 5 ? -3.229 -0.915 8.280 1.00 93.03 5 A 1 ATOM 46 N N . ALA A 1 6 ? -1.633 -1.963 5.331 1.00 94.62 6 A 1 ATOM 47 C CA . ALA A 1 6 ? -1.349 -2.733 4.120 1.00 94.63 6 A 1 ATOM 48 C C . ALA A 1 6 ? -1.612 -1.905 2.863 1.00 95.55 6 A 1 ATOM 49 O O . ALA A 1 6 ? -0.845 -1.951 1.903 1.00 94.29 6 A 1 ATOM 50 C CB . ALA A 1 6 ? -2.200 -3.995 4.108 1.00 93.77 6 A 1 ATOM 51 N N . LEU A 1 7 ? -2.704 -1.152 2.873 1.00 94.72 7 A 1 ATOM 52 C CA . LEU A 1 7 ? -3.067 -0.305 1.740 1.00 94.58 7 A 1 ATOM 53 C C . LEU A 1 7 ? -2.035 0.802 1.531 1.00 95.49 7 A 1 ATOM 54 O O . LEU A 1 7 ? -1.651 1.099 0.401 1.00 94.78 7 A 1 ATOM 55 C CB . LEU A 1 7 ? -4.448 0.315 1.972 1.00 94.05 7 A 1 ATOM 56 C CG . LEU A 1 7 ? -5.311 0.389 0.718 1.00 88.73 7 A 1 ATOM 57 C CD1 . LEU A 1 7 ? -5.997 -0.948 0.466 1.00 85.04 7 A 1 ATOM 58 C CD2 . LEU A 1 7 ? -6.342 1.493 0.846 1.00 84.87 7 A 1 ATOM 59 N N . LEU A 1 8 ? -1.594 1.408 2.618 1.00 95.04 8 A 1 ATOM 60 C CA . LEU A 1 8 ? -0.605 2.483 2.563 1.00 94.95 8 A 1 ATOM 61 C C . LEU A 1 8 ? 0.725 1.977 2.019 1.00 95.76 8 A 1 ATOM 62 O O . LEU A 1 8 ? 1.346 2.619 1.168 1.00 95.43 8 A 1 ATOM 63 C CB . LEU A 1 8 ? -0.404 3.077 3.961 1.00 94.71 8 A 1 ATOM 64 C CG . LEU A 1 8 ? -1.188 4.357 4.221 1.00 89.62 8 A 1 ATOM 65 C CD1 . LEU A 1 8 ? -1.347 4.589 5.719 1.00 86.05 8 A 1 ATOM 66 C CD2 . LEU A 1 8 ? -0.483 5.541 3.580 1.00 86.37 8 A 1 ATOM 67 N N . LEU A 1 9 ? 1.164 0.829 2.501 1.00 95.36 9 A 1 ATOM 68 C CA . LEU A 1 9 ? 2.422 0.229 2.064 1.00 94.98 9 A 1 ATOM 69 C C . LEU A 1 9 ? 2.349 -0.170 0.592 1.00 95.73 9 A 1 ATOM 70 O O . LEU A 1 9 ? 3.314 0.010 -0.155 1.00 95.32 9 A 1 ATOM 71 C CB . LEU A 1 9 ? 2.739 -0.994 2.926 1.00 94.43 9 A 1 ATOM 72 C CG . LEU A 1 9 ? 3.166 -0.673 4.357 1.00 88.86 9 A 1 ATOM 73 C CD1 . LEU A 1 9 ? 3.054 -1.912 5.227 1.00 86.46 9 A 1 ATOM 74 C CD2 . LEU A 1 9 ? 4.602 -0.154 4.369 1.00 86.62 9 A 1 ATOM 75 N N . LEU A 1 10 ? 1.210 -0.696 0.169 1.00 95.79 10 A 1 ATOM 76 C CA . LEU A 1 10 ? 1.010 -1.108 -1.215 1.00 95.36 10 A 1 ATOM 77 C C . LEU A 1 10 ? 1.005 0.098 -2.145 1.00 96.01 10 A 1 ATOM 78 O O . LEU A 1 10 ? 1.565 0.062 -3.236 1.00 95.12 10 A 1 ATOM 79 C CB . LEU A 1 10 ? -0.310 -1.880 -1.341 1.00 95.00 10 A 1 ATOM 80 C CG . LEU A 1 10 ? -0.153 -3.398 -1.460 1.00 90.87 10 A 1 ATOM 81 C CD1 . LEU A 1 10 ? 0.544 -3.754 -2.762 1.00 87.60 10 A 1 ATOM 82 C CD2 . LEU A 1 10 ? 0.617 -3.942 -0.271 1.00 87.67 10 A 1 ATOM 83 N N . CYS A 1 11 ? 0.370 1.170 -1.706 1.00 95.14 11 A 1 ATOM 84 C CA . CYS A 1 11 ? 0.293 2.399 -2.494 1.00 95.01 11 A 1 ATOM 85 C C . CYS A 1 11 ? 1.685 2.985 -2.726 1.00 95.34 11 A 1 ATOM 86 O O . CYS A 1 11 ? 2.013 3.403 -3.836 1.00 93.51 11 A 1 ATOM 87 C CB . CYS A 1 11 ? -0.589 3.424 -1.776 1.00 93.89 11 A 1 ATOM 88 S SG . CYS A 1 11 ? -1.277 4.660 -2.884 1.00 89.75 11 A 1 ATOM 89 N N . LEU A 1 12 ? 2.496 3.016 -1.675 1.00 95.62 12 A 1 ATOM 90 C CA . LEU A 1 12 ? 3.852 3.550 -1.762 1.00 95.31 12 A 1 ATOM 91 C C . LEU A 1 12 ? 4.732 2.669 -2.644 1.00 95.97 12 A 1 ATOM 92 O O . LEU A 1 12 ? 5.520 3.174 -3.447 1.00 95.23 12 A 1 ATOM 93 C CB . LEU A 1 12 ? 4.457 3.656 -0.359 1.00 94.83 12 A 1 ATOM 94 C CG . LEU A 1 12 ? 3.987 4.863 0.446 1.00 91.40 12 A 1 ATOM 95 C CD1 . LEU A 1 12 ? 4.174 4.616 1.934 1.00 87.68 12 A 1 ATOM 96 C CD2 . LEU A 1 12 ? 4.752 6.106 0.018 1.00 86.96 12 A 1 ATOM 97 N N . SER A 1 13 ? 4.604 1.363 -2.498 1.00 95.87 13 A 1 ATOM 98 C CA . SER A 1 13 ? 5.386 0.404 -3.277 1.00 95.59 13 A 1 ATOM 99 C C . SER A 1 13 ? 5.075 0.497 -4.767 1.00 95.69 13 A 1 ATOM 100 O O . SER A 1 13 ? 5.965 0.366 -5.605 1.00 92.94 13 A 1 ATOM 101 C CB . SER A 1 13 ? 5.119 -1.011 -2.769 1.00 93.75 13 A 1 ATOM 102 O OG . SER A 1 13 ? 5.784 -1.240 -1.544 1.00 83.56 13 A 1 ATOM 103 N N . GLY A 1 14 ? 3.822 0.725 -5.102 1.00 94.81 14 A 1 ATOM 104 C CA . GLY A 1 14 ? 3.411 0.832 -6.499 1.00 94.36 14 A 1 ATOM 105 C C . GLY A 1 14 ? 3.495 2.247 -7.041 1.00 95.13 14 A 1 ATOM 106 O O . GLY A 1 14 ? 3.665 2.448 -8.241 1.00 93.32 14 A 1 ATOM 107 N N . CYS A 1 15 ? 3.374 3.240 -6.171 1.00 92.89 15 A 1 ATOM 108 C CA . CYS A 1 15 ? 3.435 4.647 -6.567 1.00 92.84 15 A 1 ATOM 109 C C . CYS A 1 15 ? 4.851 5.065 -6.967 1.00 93.39 15 A 1 ATOM 110 O O . CYS A 1 15 ? 5.050 5.651 -8.027 1.00 90.11 15 A 1 ATOM 111 C CB . CYS A 1 15 ? 2.929 5.539 -5.428 1.00 90.33 15 A 1 ATOM 112 S SG . CYS A 1 15 ? 1.136 5.752 -5.454 1.00 85.82 15 A 1 ATOM 113 N N . LEU A 1 16 ? 5.824 4.787 -6.098 1.00 92.64 16 A 1 ATOM 114 C CA . LEU A 1 16 ? 7.220 5.139 -6.363 1.00 91.75 16 A 1 ATOM 115 C C . LEU A 1 16 ? 7.939 4.072 -7.180 1.00 92.58 16 A 1 ATOM 116 O O . LEU A 1 16 ? 8.866 4.371 -7.936 1.00 90.06 16 A 1 ATOM 117 C CB . LEU A 1 16 ? 7.952 5.368 -5.033 1.00 89.79 16 A 1 ATOM 118 C CG . LEU A 1 16 ? 8.240 4.092 -4.250 1.00 86.27 16 A 1 ATOM 119 C CD1 . LEU A 1 16 ? 9.728 3.770 -4.299 1.00 80.56 16 A 1 ATOM 120 C CD2 . LEU A 1 16 ? 7.801 4.251 -2.807 1.00 77.53 16 A 1 ATOM 121 N N . SER A 1 17 ? 7.532 2.828 -7.028 1.00 88.39 17 A 1 ATOM 122 C CA . SER A 1 17 ? 8.147 1.707 -7.731 1.00 86.25 17 A 1 ATOM 123 C C . SER A 1 17 ? 7.555 1.513 -9.119 1.00 83.86 17 A 1 ATOM 124 O O . SER A 1 17 ? 6.430 1.973 -9.365 1.00 76.50 17 A 1 ATOM 125 C CB . SER A 1 17 ? 7.983 0.430 -6.906 1.00 80.51 17 A 1 ATOM 126 O OG . SER A 1 17 ? 8.701 0.513 -5.694 1.00 74.67 17 A 1 ATOM 127 O OXT . SER A 1 17 ? 8.199 0.856 -9.961 1.00 76.18 17 A 1 #