# 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_spkb20586 # _entry.id spkb20586 # 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 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" "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" "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 THR 2 1 n MET 3 1 n GLN 4 1 n LEU 5 1 n GLY 6 1 n LEU 7 1 n ALA 8 1 n LEU 9 1 n VAL 10 1 n LEU 11 1 n GLY 12 1 n VAL 13 1 n ALA 14 1 n MET 15 1 n CYS 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 @ 2025-07-09 14:33:38)" _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 94.55 _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 84.39 1 1 A THR 2 2 91.20 1 2 A MET 3 2 93.45 1 3 A GLN 4 2 92.93 1 4 A LEU 5 2 95.81 1 5 A GLY 6 2 97.58 1 6 A LEU 7 2 95.86 1 7 A ALA 8 2 98.01 1 8 A LEU 9 2 96.75 1 9 A VAL 10 2 97.90 1 10 A LEU 11 2 96.49 1 11 A GLY 12 2 97.40 1 12 A VAL 13 2 97.47 1 13 A ALA 14 2 97.94 1 14 A MET 15 2 93.98 1 15 A CYS 16 2 91.24 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 THR . 2 A 2 A 3 1 n MET . 3 A 3 A 4 1 n GLN . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n GLY . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n VAL . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n GLY . 12 A 12 A 13 1 n VAL . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n MET . 15 A 15 A 16 1 n CYS . 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 ? -0.474 -11.880 3.145 1.00 89.48 1 A 1 ATOM 2 C CA . MET A 1 1 ? -0.946 -10.761 3.970 1.00 89.95 1 A 1 ATOM 3 C C . MET A 1 1 ? -1.919 -9.904 3.172 1.00 91.23 1 A 1 ATOM 4 O O . MET A 1 1 ? -1.530 -8.925 2.541 1.00 89.71 1 A 1 ATOM 5 C CB . MET A 1 1 ? 0.234 -9.906 4.437 1.00 85.48 1 A 1 ATOM 6 C CG . MET A 1 1 ? 1.181 -10.665 5.349 1.00 80.78 1 A 1 ATOM 7 S SD . MET A 1 1 ? 2.579 -9.656 5.866 1.00 79.46 1 A 1 ATOM 8 C CE . MET A 1 1 ? 3.418 -10.818 6.916 1.00 69.02 1 A 1 ATOM 9 N N . THR A 1 2 ? -3.189 -10.298 3.198 1.00 91.64 2 A 1 ATOM 10 C CA . THR A 1 2 ? -4.224 -9.578 2.458 1.00 93.91 2 A 1 ATOM 11 C C . THR A 1 2 ? -4.384 -8.143 2.950 1.00 94.97 2 A 1 ATOM 12 O O . THR A 1 2 ? -4.792 -7.261 2.193 1.00 93.13 2 A 1 ATOM 13 C CB . THR A 1 2 ? -5.566 -10.314 2.560 1.00 91.64 2 A 1 ATOM 14 O OG1 . THR A 1 2 ? -6.530 -9.676 1.723 1.00 86.73 2 A 1 ATOM 15 C CG2 . THR A 1 2 ? -6.077 -10.325 3.989 1.00 86.40 2 A 1 ATOM 16 N N . MET A 1 3 ? -4.052 -7.924 4.226 1.00 96.58 3 A 1 ATOM 17 C CA . MET A 1 3 ? -4.129 -6.586 4.808 1.00 96.83 3 A 1 ATOM 18 C C . MET A 1 3 ? -3.201 -5.617 4.083 1.00 97.37 3 A 1 ATOM 19 O O . MET A 1 3 ? -3.445 -4.411 4.047 1.00 96.50 3 A 1 ATOM 20 C CB . MET A 1 3 ? -3.763 -6.637 6.293 1.00 95.98 3 A 1 ATOM 21 C CG . MET A 1 3 ? -4.883 -7.209 7.149 1.00 93.13 3 A 1 ATOM 22 S SD . MET A 1 3 ? -6.250 -6.066 7.284 1.00 90.46 3 A 1 ATOM 23 C CE . MET A 1 3 ? -7.256 -6.901 8.493 1.00 80.79 3 A 1 ATOM 24 N N . GLN A 1 4 ? -2.132 -6.159 3.493 1.00 96.22 4 A 1 ATOM 25 C CA . GLN A 1 4 ? -1.168 -5.347 2.768 1.00 97.12 4 A 1 ATOM 26 C C . GLN A 1 4 ? -1.817 -4.673 1.571 1.00 97.60 4 A 1 ATOM 27 O O . GLN A 1 4 ? -1.388 -3.600 1.147 1.00 96.76 4 A 1 ATOM 28 C CB . GLN A 1 4 ? 0.010 -6.201 2.307 1.00 96.11 4 A 1 ATOM 29 C CG . GLN A 1 4 ? 0.785 -6.808 3.450 1.00 92.57 4 A 1 ATOM 30 C CD . GLN A 1 4 ? 1.353 -5.751 4.380 1.00 90.84 4 A 1 ATOM 31 O OE1 . GLN A 1 4 ? 0.790 -5.467 5.426 1.00 84.79 4 A 1 ATOM 32 N NE2 . GLN A 1 4 ? 2.452 -5.148 3.984 1.00 84.37 4 A 1 ATOM 33 N N . LEU A 1 5 ? -2.851 -5.297 1.029 1.00 97.15 5 A 1 ATOM 34 C CA . LEU A 1 5 ? -3.557 -4.733 -0.117 1.00 97.34 5 A 1 ATOM 35 C C . LEU A 1 5 ? -4.165 -3.384 0.239 1.00 97.74 5 A 1 ATOM 36 O O . LEU A 1 5 ? -4.107 -2.439 -0.550 1.00 97.08 5 A 1 ATOM 37 C CB . LEU A 1 5 ? -4.653 -5.696 -0.580 1.00 97.00 5 A 1 ATOM 38 C CG . LEU A 1 5 ? -4.126 -6.989 -1.199 1.00 95.06 5 A 1 ATOM 39 C CD1 . LEU A 1 5 ? -5.265 -7.965 -1.427 1.00 93.13 5 A 1 ATOM 40 C CD2 . LEU A 1 5 ? -3.413 -6.693 -2.507 1.00 92.01 5 A 1 ATOM 41 N N . GLY A 1 6 ? -4.744 -3.304 1.435 1.00 97.29 6 A 1 ATOM 42 C CA . GLY A 1 6 ? -5.329 -2.053 1.899 1.00 97.38 6 A 1 ATOM 43 C C . GLY A 1 6 ? -4.273 -0.997 2.147 1.00 97.93 6 A 1 ATOM 44 O O . GLY A 1 6 ? -4.394 0.141 1.692 1.00 97.72 6 A 1 ATOM 45 N N . LEU A 1 7 ? -3.221 -1.394 2.864 1.00 97.55 7 A 1 ATOM 46 C CA . LEU A 1 7 ? -2.128 -0.475 3.166 1.00 97.63 7 A 1 ATOM 47 C C . LEU A 1 7 ? -1.411 -0.049 1.892 1.00 98.07 7 A 1 ATOM 48 O O . LEU A 1 7 ? -1.003 1.102 1.756 1.00 97.81 7 A 1 ATOM 49 C CB . LEU A 1 7 ? -1.138 -1.139 4.125 1.00 97.18 7 A 1 ATOM 50 C CG . LEU A 1 7 ? -1.686 -1.356 5.533 1.00 93.86 7 A 1 ATOM 51 C CD1 . LEU A 1 7 ? -0.723 -2.209 6.342 1.00 92.67 7 A 1 ATOM 52 C CD2 . LEU A 1 7 ? -1.924 -0.025 6.223 1.00 92.09 7 A 1 ATOM 53 N N . ALA A 1 8 ? -1.266 -0.982 0.960 1.00 97.97 8 A 1 ATOM 54 C CA . ALA A 1 8 ? -0.610 -0.696 -0.309 1.00 98.06 8 A 1 ATOM 55 C C . ALA A 1 8 ? -1.371 0.377 -1.074 1.00 98.32 8 A 1 ATOM 56 O O . ALA A 1 8 ? -0.772 1.233 -1.724 1.00 97.91 8 A 1 ATOM 57 C CB . ALA A 1 8 ? -0.512 -1.964 -1.146 1.00 97.77 8 A 1 ATOM 58 N N . LEU A 1 9 ? -2.696 0.323 -0.989 1.00 98.01 9 A 1 ATOM 59 C CA . LEU A 1 9 ? -3.530 1.317 -1.657 1.00 98.04 9 A 1 ATOM 60 C C . LEU A 1 9 ? -3.293 2.700 -1.066 1.00 98.38 9 A 1 ATOM 61 O O . LEU A 1 9 ? -3.143 3.680 -1.797 1.00 98.12 9 A 1 ATOM 62 C CB . LEU A 1 9 ? -5.007 0.942 -1.516 1.00 97.77 9 A 1 ATOM 63 C CG . LEU A 1 9 ? -5.974 1.928 -2.175 1.00 95.36 9 A 1 ATOM 64 C CD1 . LEU A 1 9 ? -5.741 1.983 -3.673 1.00 94.19 9 A 1 ATOM 65 C CD2 . LEU A 1 9 ? -7.409 1.531 -1.872 1.00 94.16 9 A 1 ATOM 66 N N . VAL A 1 10 ? -3.263 2.761 0.268 1.00 98.17 10 A 1 ATOM 67 C CA . VAL A 1 10 ? -3.027 4.029 0.960 1.00 98.27 10 A 1 ATOM 68 C C . VAL A 1 10 ? -1.676 4.603 0.564 1.00 98.47 10 A 1 ATOM 69 O O . VAL A 1 10 ? -1.560 5.791 0.250 1.00 98.28 10 A 1 ATOM 70 C CB . VAL A 1 10 ? -3.087 3.849 2.487 1.00 97.93 10 A 1 ATOM 71 C CG1 . VAL A 1 10 ? -2.777 5.161 3.196 1.00 97.06 10 A 1 ATOM 72 C CG2 . VAL A 1 10 ? -4.456 3.339 2.905 1.00 97.14 10 A 1 ATOM 73 N N . LEU A 1 11 ? -0.658 3.743 0.575 1.00 97.81 11 A 1 ATOM 74 C CA . LEU A 1 11 ? 0.685 4.165 0.201 1.00 97.76 11 A 1 ATOM 75 C C . LEU A 1 11 ? 0.720 4.597 -1.256 1.00 98.11 11 A 1 ATOM 76 O O . LEU A 1 11 ? 1.396 5.560 -1.612 1.00 97.69 11 A 1 ATOM 77 C CB . LEU A 1 11 ? 1.672 3.023 0.434 1.00 97.40 11 A 1 ATOM 78 C CG . LEU A 1 11 ? 1.891 2.687 1.909 1.00 95.41 11 A 1 ATOM 79 C CD1 . LEU A 1 11 ? 2.680 1.390 2.040 1.00 93.99 11 A 1 ATOM 80 C CD2 . LEU A 1 11 ? 2.617 3.825 2.608 1.00 93.72 11 A 1 ATOM 81 N N . GLY A 1 12 ? -0.018 3.883 -2.093 1.00 97.12 12 A 1 ATOM 82 C CA . GLY A 1 12 ? -0.088 4.219 -3.506 1.00 97.13 12 A 1 ATOM 83 C C . GLY A 1 12 ? -0.668 5.601 -3.721 1.00 97.81 12 A 1 ATOM 84 O O . GLY A 1 12 ? -0.127 6.397 -4.487 1.00 97.53 12 A 1 ATOM 85 N N . VAL A 1 13 ? -1.769 5.890 -3.026 1.00 98.13 13 A 1 ATOM 86 C CA . VAL A 1 13 ? -2.410 7.202 -3.131 1.00 98.18 13 A 1 ATOM 87 C C . VAL A 1 13 ? -1.467 8.300 -2.662 1.00 98.41 13 A 1 ATOM 88 O O . VAL A 1 13 ? -1.378 9.362 -3.281 1.00 98.02 13 A 1 ATOM 89 C CB . VAL A 1 13 ? -3.706 7.247 -2.307 1.00 97.73 13 A 1 ATOM 90 C CG1 . VAL A 1 13 ? -4.310 8.645 -2.332 1.00 95.73 13 A 1 ATOM 91 C CG2 . VAL A 1 13 ? -4.705 6.239 -2.848 1.00 96.09 13 A 1 ATOM 92 N N . ALA A 1 14 ? -0.772 8.038 -1.553 1.00 98.09 14 A 1 ATOM 93 C CA . ALA A 1 14 ? 0.171 9.006 -1.001 1.00 98.12 14 A 1 ATOM 94 C C . ALA A 1 14 ? 1.343 9.243 -1.945 1.00 98.26 14 A 1 ATOM 95 O O . ALA A 1 14 ? 1.904 10.341 -1.984 1.00 97.64 14 A 1 ATOM 96 C CB . ALA A 1 14 ? 0.684 8.527 0.354 1.00 97.59 14 A 1 ATOM 97 N N . MET A 1 15 ? 1.718 8.208 -2.689 1.00 97.84 15 A 1 ATOM 98 C CA . MET A 1 15 ? 2.839 8.289 -3.622 1.00 97.64 15 A 1 ATOM 99 C C . MET A 1 15 ? 2.377 8.385 -5.075 1.00 97.73 15 A 1 ATOM 100 O O . MET A 1 15 ? 3.173 8.219 -5.997 1.00 96.68 15 A 1 ATOM 101 C CB . MET A 1 15 ? 3.753 7.078 -3.453 1.00 97.06 15 A 1 ATOM 102 C CG . MET A 1 15 ? 4.457 7.054 -2.106 1.00 94.07 15 A 1 ATOM 103 S SD . MET A 1 15 ? 5.566 5.642 -1.945 1.00 89.56 15 A 1 ATOM 104 C CE . MET A 1 15 ? 6.380 6.061 -0.412 1.00 81.29 15 A 1 ATOM 105 N N . CYS A 1 16 ? 1.106 8.676 -5.270 1.00 95.99 16 A 1 ATOM 106 C CA . CYS A 1 16 ? 0.566 8.755 -6.625 1.00 94.86 16 A 1 ATOM 107 C C . CYS A 1 16 ? 0.416 10.203 -7.057 1.00 94.02 16 A 1 ATOM 108 O O . CYS A 1 16 ? -0.711 10.721 -7.099 1.00 91.45 16 A 1 ATOM 109 C CB . CYS A 1 16 ? -0.767 8.029 -6.718 1.00 91.35 16 A 1 ATOM 110 S SG . CYS A 1 16 ? -1.383 7.917 -8.408 1.00 85.62 16 A 1 ATOM 111 O OXT . CYS A 1 16 ? 1.473 10.821 -7.364 1.00 85.40 16 A 1 #