# 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_spkb16741 # _entry.id spkb16741 # 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" "C5 H9 N O4" 147.129 GLU y "GLUTAMIC ACID" C(CC(=O)O)[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 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" "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" "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" # _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 THR 3 1 n GLU 4 1 n SER 5 1 n LYS 6 1 n CYS 7 1 n PRO 8 1 n PHE 9 1 n ALA 10 1 n GLY 11 1 n GLY 12 1 n ALA 13 1 n TYR 14 1 n ALA 15 # _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 21:00:06)" _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 75.32 _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 69.42 1 1 A SER 2 2 74.09 1 2 A THR 3 2 74.00 1 3 A GLU 4 2 69.36 1 4 A SER 5 2 78.50 1 5 A LYS 6 2 75.51 1 6 A CYS 7 2 78.60 1 7 A PRO 8 2 82.28 1 8 A PHE 9 2 79.46 1 9 A ALA 10 2 77.29 1 10 A GLY 11 2 78.00 1 11 A GLY 12 2 79.66 1 12 A ALA 13 2 77.88 1 13 A TYR 14 2 71.62 1 14 A ALA 15 2 71.47 1 15 # _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 THR . 3 A 3 A 4 1 n GLU . 4 A 4 A 5 1 n SER . 5 A 5 A 6 1 n LYS . 6 A 6 A 7 1 n CYS . 7 A 7 A 8 1 n PRO . 8 A 8 A 9 1 n PHE . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n GLY . 11 A 11 A 12 1 n GLY . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n TYR . 14 A 14 A 15 1 n ALA . 15 A 15 # _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 ? 12.981 -3.814 1.729 1.00 71.77 1 A 1 ATOM 2 C CA . MET A 1 1 ? 11.614 -3.409 2.107 1.00 75.27 1 A 1 ATOM 3 C C . MET A 1 1 ? 10.851 -2.922 0.880 1.00 77.10 1 A 1 ATOM 4 O O . MET A 1 1 ? 11.160 -1.871 0.330 1.00 73.93 1 A 1 ATOM 5 C CB . MET A 1 1 ? 11.650 -2.288 3.151 1.00 70.13 1 A 1 ATOM 6 C CG . MET A 1 1 ? 12.285 -2.719 4.463 1.00 67.48 1 A 1 ATOM 7 S SD . MET A 1 1 ? 12.358 -1.382 5.672 1.00 62.57 1 A 1 ATOM 8 C CE . MET A 1 1 ? 13.101 -2.249 7.047 1.00 57.13 1 A 1 ATOM 9 N N . SER A 1 2 ? 9.874 -3.692 0.448 1.00 72.86 2 A 1 ATOM 10 C CA . SER A 1 2 ? 9.049 -3.325 -0.701 1.00 76.87 2 A 1 ATOM 11 C C . SER A 1 2 ? 7.889 -2.427 -0.269 1.00 79.79 2 A 1 ATOM 12 O O . SER A 1 2 ? 7.715 -2.139 0.915 1.00 77.07 2 A 1 ATOM 13 C CB . SER A 1 2 ? 8.515 -4.586 -1.375 1.00 71.60 2 A 1 ATOM 14 O OG . SER A 1 2 ? 7.792 -5.376 -0.469 1.00 66.32 2 A 1 ATOM 15 N N . THR A 1 3 ? 7.090 -1.994 -1.237 1.00 74.07 3 A 1 ATOM 16 C CA . THR A 1 3 ? 5.944 -1.127 -0.963 1.00 76.52 3 A 1 ATOM 17 C C . THR A 1 3 ? 4.860 -1.896 -0.216 1.00 77.69 3 A 1 ATOM 18 O O . THR A 1 3 ? 4.107 -2.676 -0.805 1.00 75.28 3 A 1 ATOM 19 C CB . THR A 1 3 ? 5.367 -0.553 -2.263 1.00 74.53 3 A 1 ATOM 20 O OG1 . THR A 1 3 ? 5.138 -1.596 -3.202 1.00 70.01 3 A 1 ATOM 21 C CG2 . THR A 1 3 ? 6.321 0.463 -2.873 1.00 69.87 3 A 1 ATOM 22 N N . GLU A 1 4 ? 4.784 -1.670 1.092 1.00 71.71 4 A 1 ATOM 23 C CA . GLU A 1 4 ? 3.798 -2.333 1.935 1.00 74.32 4 A 1 ATOM 24 C C . GLU A 1 4 ? 2.600 -1.423 2.178 1.00 76.63 4 A 1 ATOM 25 O O . GLU A 1 4 ? 2.757 -0.264 2.559 1.00 73.87 4 A 1 ATOM 26 C CB . GLU A 1 4 ? 4.440 -2.731 3.266 1.00 71.58 4 A 1 ATOM 27 C CG . GLU A 1 4 ? 3.497 -3.484 4.178 1.00 66.98 4 A 1 ATOM 28 C CD . GLU A 1 4 ? 4.148 -3.820 5.503 1.00 65.91 4 A 1 ATOM 29 O OE1 . GLU A 1 4 ? 4.865 -4.823 5.577 1.00 58.99 4 A 1 ATOM 30 O OE2 . GLU A 1 4 ? 3.950 -3.053 6.459 1.00 64.23 4 A 1 ATOM 31 N N . SER A 1 5 ? 1.403 -1.956 1.951 1.00 80.67 5 A 1 ATOM 32 C CA . SER A 1 5 ? 0.179 -1.190 2.156 1.00 80.15 5 A 1 ATOM 33 C C . SER A 1 5 ? -0.182 -1.167 3.641 1.00 81.62 5 A 1 ATOM 34 O O . SER A 1 5 ? -0.637 -2.168 4.186 1.00 78.47 5 A 1 ATOM 35 C CB . SER A 1 5 ? -0.966 -1.782 1.341 1.00 77.57 5 A 1 ATOM 36 O OG . SER A 1 5 ? -2.142 -1.031 1.505 1.00 72.54 5 A 1 ATOM 37 N N . LYS A 1 6 ? 0.034 -0.033 4.293 1.00 78.14 6 A 1 ATOM 38 C CA . LYS A 1 6 ? -0.268 0.124 5.713 1.00 78.84 6 A 1 ATOM 39 C C . LYS A 1 6 ? -1.772 0.133 5.956 1.00 78.73 6 A 1 ATOM 40 O O . LYS A 1 6 ? -2.261 -0.474 6.906 1.00 76.32 6 A 1 ATOM 41 C CB . LYS A 1 6 ? 0.356 1.411 6.241 1.00 77.23 6 A 1 ATOM 42 C CG . LYS A 1 6 ? 1.867 1.481 6.072 1.00 76.11 6 A 1 ATOM 43 C CD . LYS A 1 6 ? 2.579 0.362 6.816 1.00 75.57 6 A 1 ATOM 44 C CE . LYS A 1 6 ? 4.082 0.459 6.646 1.00 71.77 6 A 1 ATOM 45 N NZ . LYS A 1 6 ? 4.786 -0.638 7.348 1.00 66.90 6 A 1 ATOM 46 N N . CYS A 1 7 ? -2.511 0.817 5.102 1.00 79.95 7 A 1 ATOM 47 C CA . CYS A 1 7 ? -3.962 0.904 5.202 1.00 80.57 7 A 1 ATOM 48 C C . CYS A 1 7 ? -4.619 0.277 3.976 1.00 81.13 7 A 1 ATOM 49 O O . CYS A 1 7 ? -4.574 0.858 2.892 1.00 77.51 7 A 1 ATOM 50 C CB . CYS A 1 7 ? -4.391 2.365 5.339 1.00 77.75 7 A 1 ATOM 51 S SG . CYS A 1 7 ? -3.655 3.172 6.781 1.00 74.68 7 A 1 ATOM 52 N N . PRO A 1 8 ? -5.236 -0.901 4.131 1.00 82.14 8 A 1 ATOM 53 C CA . PRO A 1 8 ? -5.875 -1.618 3.026 1.00 82.45 8 A 1 ATOM 54 C C . PRO A 1 8 ? -7.244 -1.049 2.644 1.00 83.54 8 A 1 ATOM 55 O O . PRO A 1 8 ? -8.176 -1.800 2.350 1.00 80.21 8 A 1 ATOM 56 C CB . PRO A 1 8 ? -6.003 -3.050 3.558 1.00 80.55 8 A 1 ATOM 57 C CG . PRO A 1 8 ? -6.152 -2.872 5.031 1.00 81.63 8 A 1 ATOM 58 C CD . PRO A 1 8 ? -5.303 -1.664 5.381 1.00 85.43 8 A 1 ATOM 59 N N . PHE A 1 9 ? -7.372 0.266 2.633 1.00 80.47 9 A 1 ATOM 60 C CA . PHE A 1 9 ? -8.629 0.913 2.265 1.00 81.21 9 A 1 ATOM 61 C C . PHE A 1 9 ? -8.768 0.947 0.740 1.00 82.28 9 A 1 ATOM 62 O O . PHE A 1 9 ? -8.225 1.802 0.055 1.00 79.27 9 A 1 ATOM 63 C CB . PHE A 1 9 ? -8.713 2.322 2.851 1.00 80.06 9 A 1 ATOM 64 C CG . PHE A 1 9 ? -7.506 3.181 2.574 1.00 79.71 9 A 1 ATOM 65 C CD1 . PHE A 1 9 ? -7.417 3.916 1.402 1.00 78.71 9 A 1 ATOM 66 C CD2 . PHE A 1 9 ? -6.469 3.251 3.492 1.00 77.79 9 A 1 ATOM 67 C CE1 . PHE A 1 9 ? -6.308 4.698 1.144 1.00 78.31 9 A 1 ATOM 68 C CE2 . PHE A 1 9 ? -5.354 4.033 3.234 1.00 78.39 9 A 1 ATOM 69 C CZ . PHE A 1 9 ? -5.279 4.752 2.059 1.00 77.82 9 A 1 ATOM 70 N N . ALA A 1 10 ? -9.529 -0.027 0.210 1.00 77.98 10 A 1 ATOM 71 C CA . ALA A 1 10 ? -9.743 -0.123 -1.238 1.00 78.52 10 A 1 ATOM 72 C C . ALA A 1 10 ? -8.430 -0.054 -2.008 1.00 79.66 10 A 1 ATOM 73 O O . ALA A 1 10 ? -8.303 0.683 -2.982 1.00 74.39 10 A 1 ATOM 74 C CB . ALA A 1 10 ? -10.703 0.972 -1.708 1.00 75.92 10 A 1 ATOM 75 N N . GLY A 1 11 ? -7.457 -0.820 -1.555 1.00 78.01 11 A 1 ATOM 76 C CA . GLY A 1 11 ? -6.131 -0.805 -2.161 1.00 78.03 11 A 1 ATOM 77 C C . GLY A 1 11 ? -6.142 -1.120 -3.638 1.00 80.10 11 A 1 ATOM 78 O O . GLY A 1 11 ? -5.375 -0.546 -4.405 1.00 75.87 11 A 1 ATOM 79 N N . GLY A 1 12 ? -7.024 -2.033 -4.063 1.00 78.76 12 A 1 ATOM 80 C CA . GLY A 1 12 ? -7.127 -2.396 -5.475 1.00 79.70 12 A 1 ATOM 81 C C . GLY A 1 12 ? -7.623 -1.260 -6.345 1.00 81.87 12 A 1 ATOM 82 O O . GLY A 1 12 ? -7.111 -1.042 -7.442 1.00 78.30 12 A 1 ATOM 83 N N . ALA A 1 13 ? -8.627 -0.534 -5.875 1.00 78.20 13 A 1 ATOM 84 C CA . ALA A 1 13 ? -9.197 0.586 -6.629 1.00 79.31 13 A 1 ATOM 85 C C . ALA A 1 13 ? -8.425 1.884 -6.410 1.00 80.04 13 A 1 ATOM 86 O O . ALA A 1 13 ? -8.315 2.710 -7.312 1.00 75.93 13 A 1 ATOM 87 C CB . ALA A 1 13 ? -10.661 0.784 -6.247 1.00 75.91 13 A 1 ATOM 88 N N . TYR A 1 14 ? -7.901 2.066 -5.208 1.00 75.72 14 A 1 ATOM 89 C CA . TYR A 1 14 ? -7.165 3.280 -4.857 1.00 75.82 14 A 1 ATOM 90 C C . TYR A 1 14 ? -5.743 3.236 -5.399 1.00 76.45 14 A 1 ATOM 91 O O . TYR A 1 14 ? -5.311 4.139 -6.117 1.00 70.31 14 A 1 ATOM 92 C CB . TYR A 1 14 ? -7.152 3.455 -3.337 1.00 72.26 14 A 1 ATOM 93 C CG . TYR A 1 14 ? -6.590 4.789 -2.899 1.00 73.01 14 A 1 ATOM 94 C CD1 . TYR A 1 14 ? -7.382 5.928 -2.930 1.00 72.07 14 A 1 ATOM 95 C CD2 . TYR A 1 14 ? -5.281 4.903 -2.455 1.00 71.35 14 A 1 ATOM 96 C CE1 . TYR A 1 14 ? -6.874 7.154 -2.533 1.00 69.28 14 A 1 ATOM 97 C CE2 . TYR A 1 14 ? -4.766 6.132 -2.061 1.00 69.68 14 A 1 ATOM 98 C CZ . TYR A 1 14 ? -5.566 7.252 -2.099 1.00 69.35 14 A 1 ATOM 99 O OH . TYR A 1 14 ? -5.061 8.462 -1.711 1.00 64.15 14 A 1 ATOM 100 N N . ALA A 1 15 ? -5.004 2.179 -5.041 1.00 75.64 15 A 1 ATOM 101 C CA . ALA A 1 15 ? -3.620 2.033 -5.484 1.00 75.40 15 A 1 ATOM 102 C C . ALA A 1 15 ? -3.262 0.562 -5.609 1.00 72.61 15 A 1 ATOM 103 O O . ALA A 1 15 ? -2.892 0.126 -6.722 1.00 68.00 15 A 1 ATOM 104 C CB . ALA A 1 15 ? -2.679 2.738 -4.506 1.00 69.69 15 A 1 ATOM 105 O OXT . ALA A 1 15 ? -3.362 -0.145 -4.610 1.00 67.46 15 A 1 #