# 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_spkb26024 # _entry.id spkb26024 # 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" "C6 H15 N4 O2" 175.209 ARG y ARGININE C(C[C@@H](C(=O)O)N)CNC(=[NH2+])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" "C6 H13 N O2" 131.173 ILE y ISOLEUCINE CC[C@H](C)[C@@H](C(=O)O)N ? "L-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" "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 ARG 2 1 n ILE 3 1 n GLN 4 1 n LEU 5 1 n LEU 6 1 n LEU 7 1 n VAL 8 1 n ALA 9 1 n THR 10 1 n LEU 11 1 n VAL 12 1 n ALA 13 1 n SER 14 1 n ILE 15 1 n VAL 16 1 n ALA 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 22:30:27)" _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 96.28 _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 90.62 1 1 A ARG 2 2 90.54 1 2 A ILE 3 2 97.11 1 3 A GLN 4 2 95.37 1 4 A LEU 5 2 97.69 1 5 A LEU 6 2 97.57 1 6 A LEU 7 2 97.77 1 7 A VAL 8 2 98.35 1 8 A ALA 9 2 98.69 1 9 A THR 10 2 97.92 1 10 A LEU 11 2 97.25 1 11 A VAL 12 2 98.22 1 12 A ALA 13 2 98.75 1 13 A SER 14 2 97.70 1 14 A ILE 15 2 97.19 1 15 A VAL 16 2 97.15 1 16 A ALA 17 2 93.37 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 ARG . 2 A 2 A 3 1 n ILE . 3 A 3 A 4 1 n GLN . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n VAL . 8 A 8 A 9 1 n ALA . 9 A 9 A 10 1 n THR . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n VAL . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n SER . 14 A 14 A 15 1 n ILE . 15 A 15 A 16 1 n VAL . 16 A 16 A 17 1 n ALA . 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 ? 4.682 -0.256 11.903 1.00 96.06 1 A 1 ATOM 2 C CA . MET A 1 1 ? 3.858 0.640 11.082 1.00 95.92 1 A 1 ATOM 3 C C . MET A 1 1 ? 2.945 -0.166 10.160 1.00 96.68 1 A 1 ATOM 4 O O . MET A 1 1 ? 3.292 -0.459 9.019 1.00 95.43 1 A 1 ATOM 5 C CB . MET A 1 1 ? 4.741 1.551 10.246 1.00 93.00 1 A 1 ATOM 6 C CG . MET A 1 1 ? 5.622 2.458 11.099 1.00 88.30 1 A 1 ATOM 7 S SD . MET A 1 1 ? 4.651 3.613 12.066 1.00 85.03 1 A 1 ATOM 8 C CE . MET A 1 1 ? 5.935 4.496 12.917 1.00 74.58 1 A 1 ATOM 9 N N . ARG A 1 2 ? 1.788 -0.535 10.670 1.00 97.93 2 A 1 ATOM 10 C CA . ARG A 1 2 ? 0.818 -1.311 9.900 1.00 98.10 2 A 1 ATOM 11 C C . ARG A 1 2 ? 0.086 -0.428 8.894 1.00 98.45 2 A 1 ATOM 12 O O . ARG A 1 2 ? -0.353 -0.902 7.848 1.00 97.98 2 A 1 ATOM 13 C CB . ARG A 1 2 ? -0.196 -1.964 10.843 1.00 97.17 2 A 1 ATOM 14 C CG . ARG A 1 2 ? 0.445 -2.869 11.882 1.00 93.26 2 A 1 ATOM 15 C CD . ARG A 1 2 ? -0.610 -3.454 12.798 1.00 90.55 2 A 1 ATOM 16 N NE . ARG A 1 2 ? -0.007 -4.166 13.922 1.00 84.61 2 A 1 ATOM 17 C CZ . ARG A 1 2 ? -0.701 -4.721 14.909 1.00 83.70 2 A 1 ATOM 18 N NH1 . ARG A 1 2 ? -2.022 -4.666 14.916 1.00 77.06 2 A 1 ATOM 19 N NH2 . ARG A 1 2 ? -0.077 -5.329 15.897 1.00 77.15 2 A 1 ATOM 20 N N . ILE A 1 3 ? -0.043 0.855 9.217 1.00 98.43 3 A 1 ATOM 21 C CA . ILE A 1 3 ? -0.743 1.804 8.359 1.00 98.47 3 A 1 ATOM 22 C C . ILE A 1 3 ? -0.072 1.898 6.992 1.00 98.64 3 A 1 ATOM 23 O O . ILE A 1 3 ? -0.744 2.014 5.963 1.00 98.41 3 A 1 ATOM 24 C CB . ILE A 1 3 ? -0.805 3.195 9.015 1.00 98.21 3 A 1 ATOM 25 C CG1 . ILE A 1 3 ? -1.554 3.118 10.353 1.00 96.40 3 A 1 ATOM 26 C CG2 . ILE A 1 3 ? -1.491 4.188 8.085 1.00 95.67 3 A 1 ATOM 27 C CD1 . ILE A 1 3 ? -1.460 4.407 11.161 1.00 92.66 3 A 1 ATOM 28 N N . GLN A 1 4 ? 1.257 1.823 6.989 1.00 98.73 4 A 1 ATOM 29 C CA . GLN A 1 4 ? 2.011 1.922 5.743 1.00 98.73 4 A 1 ATOM 30 C C . GLN A 1 4 ? 1.636 0.797 4.790 1.00 98.79 4 A 1 ATOM 31 O O . GLN A 1 4 ? 1.532 1.000 3.580 1.00 98.60 4 A 1 ATOM 32 C CB . GLN A 1 4 ? 3.513 1.899 6.032 1.00 98.53 4 A 1 ATOM 33 C CG . GLN A 1 4 ? 3.975 3.027 6.941 1.00 96.25 4 A 1 ATOM 34 C CD . GLN A 1 4 ? 3.611 4.397 6.394 1.00 94.10 4 A 1 ATOM 35 O OE1 . GLN A 1 4 ? 2.562 4.942 6.706 1.00 88.05 4 A 1 ATOM 36 N NE2 . GLN A 1 4 ? 4.468 4.944 5.557 1.00 86.57 4 A 1 ATOM 37 N N . LEU A 1 5 ? 1.434 -0.388 5.330 1.00 98.75 5 A 1 ATOM 38 C CA . LEU A 1 5 ? 1.060 -1.544 4.523 1.00 98.78 5 A 1 ATOM 39 C C . LEU A 1 5 ? -0.303 -1.327 3.874 1.00 98.82 5 A 1 ATOM 40 O O . LEU A 1 5 ? -0.518 -1.698 2.718 1.00 98.72 5 A 1 ATOM 41 C CB . LEU A 1 5 ? 1.030 -2.804 5.393 1.00 98.69 5 A 1 ATOM 42 C CG . LEU A 1 5 ? 2.395 -3.216 5.948 1.00 97.22 5 A 1 ATOM 43 C CD1 . LEU A 1 5 ? 2.237 -4.383 6.908 1.00 95.50 5 A 1 ATOM 44 C CD2 . LEU A 1 5 ? 3.342 -3.590 4.819 1.00 95.06 5 A 1 ATOM 45 N N . LEU A 1 6 ? -1.214 -0.724 4.621 1.00 98.80 6 A 1 ATOM 46 C CA . LEU A 1 6 ? -2.552 -0.451 4.114 1.00 98.79 6 A 1 ATOM 47 C C . LEU A 1 6 ? -2.507 0.585 2.997 1.00 98.84 6 A 1 ATOM 48 O O . LEU A 1 6 ? -3.198 0.452 1.984 1.00 98.75 6 A 1 ATOM 49 C CB . LEU A 1 6 ? -3.455 0.041 5.250 1.00 98.71 6 A 1 ATOM 50 C CG . LEU A 1 6 ? -3.713 -0.992 6.345 1.00 97.08 6 A 1 ATOM 51 C CD1 . LEU A 1 6 ? -4.483 -0.355 7.498 1.00 94.93 6 A 1 ATOM 52 C CD2 . LEU A 1 6 ? -4.494 -2.176 5.791 1.00 94.64 6 A 1 ATOM 53 N N . LEU A 1 7 ? -1.681 1.604 3.176 1.00 98.80 7 A 1 ATOM 54 C CA . LEU A 1 7 ? -1.542 2.658 2.178 1.00 98.81 7 A 1 ATOM 55 C C . LEU A 1 7 ? -0.965 2.104 0.882 1.00 98.85 7 A 1 ATOM 56 O O . LEU A 1 7 ? -1.451 2.414 -0.208 1.00 98.79 7 A 1 ATOM 57 C CB . LEU A 1 7 ? -0.643 3.774 2.720 1.00 98.73 7 A 1 ATOM 58 C CG . LEU A 1 7 ? -1.249 4.555 3.885 1.00 97.13 7 A 1 ATOM 59 C CD1 . LEU A 1 7 ? -0.226 5.523 4.460 1.00 95.52 7 A 1 ATOM 60 C CD2 . LEU A 1 7 ? -2.488 5.316 3.437 1.00 95.53 7 A 1 ATOM 61 N N . VAL A 1 8 ? 0.060 1.281 1.007 1.00 98.81 8 A 1 ATOM 62 C CA . VAL A 1 8 ? 0.689 0.673 -0.158 1.00 98.80 8 A 1 ATOM 63 C C . VAL A 1 8 ? -0.299 -0.243 -0.868 1.00 98.83 8 A 1 ATOM 64 O O . VAL A 1 8 ? -0.380 -0.254 -2.097 1.00 98.73 8 A 1 ATOM 65 C CB . VAL A 1 8 ? 1.948 -0.108 0.242 1.00 98.63 8 A 1 ATOM 66 C CG1 . VAL A 1 8 ? 2.514 -0.865 -0.951 1.00 97.40 8 A 1 ATOM 67 C CG2 . VAL A 1 8 ? 2.993 0.845 0.801 1.00 97.28 8 A 1 ATOM 68 N N . ALA A 1 9 ? -1.038 -1.011 -0.093 1.00 98.75 9 A 1 ATOM 69 C CA . ALA A 1 9 ? -2.023 -1.924 -0.652 1.00 98.73 9 A 1 ATOM 70 C C . ALA A 1 9 ? -3.075 -1.162 -1.455 1.00 98.79 9 A 1 ATOM 71 O O . ALA A 1 9 ? -3.531 -1.632 -2.498 1.00 98.63 9 A 1 ATOM 72 C CB . ALA A 1 9 ? -2.688 -2.716 0.467 1.00 98.54 9 A 1 ATOM 73 N N . THR A 1 10 ? -3.443 0.007 -0.974 1.00 98.82 10 A 1 ATOM 74 C CA . THR A 1 10 ? -4.429 0.839 -1.654 1.00 98.78 10 A 1 ATOM 75 C C . THR A 1 10 ? -3.897 1.304 -3.006 1.00 98.82 10 A 1 ATOM 76 O O . THR A 1 10 ? -4.623 1.294 -4.005 1.00 98.60 10 A 1 ATOM 77 C CB . THR A 1 10 ? -4.790 2.058 -0.803 1.00 98.58 10 A 1 ATOM 78 O OG1 . THR A 1 10 ? -5.293 1.629 0.459 1.00 96.44 10 A 1 ATOM 79 C CG2 . THR A 1 10 ? -5.843 2.904 -1.499 1.00 95.40 10 A 1 ATOM 80 N N . LEU A 1 11 ? -2.632 1.688 -3.045 1.00 98.81 11 A 1 ATOM 81 C CA . LEU A 1 11 ? -2.007 2.140 -4.280 1.00 98.77 11 A 1 ATOM 82 C C . LEU A 1 11 ? -1.952 1.014 -5.299 1.00 98.82 11 A 1 ATOM 83 O O . LEU A 1 11 ? -2.261 1.212 -6.474 1.00 98.66 11 A 1 ATOM 84 C CB . LEU A 1 11 ? -0.599 2.654 -3.995 1.00 98.64 11 A 1 ATOM 85 C CG . LEU A 1 11 ? -0.559 3.925 -3.151 1.00 95.97 11 A 1 ATOM 86 C CD1 . LEU A 1 11 ? 0.872 4.264 -2.779 1.00 93.75 11 A 1 ATOM 87 C CD2 . LEU A 1 11 ? -1.199 5.083 -3.906 1.00 94.58 11 A 1 ATOM 88 N N . VAL A 1 12 ? -1.554 -0.162 -4.844 1.00 98.81 12 A 1 ATOM 89 C CA . VAL A 1 12 ? -1.471 -1.324 -5.717 1.00 98.77 12 A 1 ATOM 90 C C . VAL A 1 12 ? -2.850 -1.676 -6.257 1.00 98.81 12 A 1 ATOM 91 O O . VAL A 1 12 ? -3.008 -1.991 -7.439 1.00 98.62 12 A 1 ATOM 92 C CB . VAL A 1 12 ? -0.870 -2.525 -4.975 1.00 98.50 12 A 1 ATOM 93 C CG1 . VAL A 1 12 ? -0.902 -3.764 -5.854 1.00 96.82 12 A 1 ATOM 94 C CG2 . VAL A 1 12 ? 0.554 -2.215 -4.553 1.00 97.23 12 A 1 ATOM 95 N N . ALA A 1 13 ? -3.839 -1.623 -5.389 1.00 98.84 13 A 1 ATOM 96 C CA . ALA A 1 13 ? -5.208 -1.930 -5.785 1.00 98.82 13 A 1 ATOM 97 C C . ALA A 1 13 ? -5.697 -0.963 -6.860 1.00 98.85 13 A 1 ATOM 98 O O . ALA A 1 13 ? -6.422 -1.355 -7.774 1.00 98.64 13 A 1 ATOM 99 C CB . ALA A 1 13 ? -6.125 -1.874 -4.570 1.00 98.62 13 A 1 ATOM 100 N N . SER A 1 14 ? -5.284 0.288 -6.763 1.00 98.88 14 A 1 ATOM 101 C CA . SER A 1 14 ? -5.669 1.307 -7.735 1.00 98.84 14 A 1 ATOM 102 C C . SER A 1 14 ? -5.087 1.007 -9.110 1.00 98.88 14 A 1 ATOM 103 O O . SER A 1 14 ? -5.708 1.291 -10.133 1.00 98.61 14 A 1 ATOM 104 C CB . SER A 1 14 ? -5.207 2.681 -7.270 1.00 98.60 14 A 1 ATOM 105 O OG . SER A 1 14 ? -5.829 3.023 -6.050 1.00 92.36 14 A 1 ATOM 106 N N . ILE A 1 15 ? -3.893 0.432 -9.132 1.00 98.67 15 A 1 ATOM 107 C CA . ILE A 1 15 ? -3.232 0.085 -10.383 1.00 98.59 15 A 1 ATOM 108 C C . ILE A 1 15 ? -3.892 -1.132 -11.019 1.00 98.66 15 A 1 ATOM 109 O O . ILE A 1 15 ? -4.133 -1.166 -12.228 1.00 98.24 15 A 1 ATOM 110 C CB . ILE A 1 15 ? -1.739 -0.190 -10.148 1.00 98.27 15 A 1 ATOM 111 C CG1 . ILE A 1 15 ? -1.046 1.082 -9.649 1.00 96.38 15 A 1 ATOM 112 C CG2 . ILE A 1 15 ? -1.083 -0.693 -11.430 1.00 96.17 15 A 1 ATOM 113 C CD1 . ILE A 1 15 ? 0.360 0.836 -9.143 1.00 92.53 15 A 1 ATOM 114 N N . VAL A 1 16 ? -4.149 -2.137 -10.202 1.00 98.64 16 A 1 ATOM 115 C CA . VAL A 1 16 ? -4.761 -3.371 -10.682 1.00 98.52 16 A 1 ATOM 116 C C . VAL A 1 16 ? -6.215 -3.150 -11.079 1.00 98.54 16 A 1 ATOM 117 O O . VAL A 1 16 ? -6.704 -3.737 -12.053 1.00 97.87 16 A 1 ATOM 118 C CB . VAL A 1 16 ? -4.672 -4.474 -9.615 1.00 97.78 16 A 1 ATOM 119 C CG1 . VAL A 1 16 ? -5.372 -5.739 -10.087 1.00 93.96 16 A 1 ATOM 120 C CG2 . VAL A 1 16 ? -3.221 -4.770 -9.286 1.00 94.74 16 A 1 ATOM 121 N N . ALA A 1 17 ? -6.903 -2.309 -10.315 1.00 97.39 17 A 1 ATOM 122 C CA . ALA A 1 17 ? -8.313 -2.030 -10.551 1.00 96.36 17 A 1 ATOM 123 C C . ALA A 1 17 ? -8.502 -0.608 -11.073 1.00 95.46 17 A 1 ATOM 124 O O . ALA A 1 17 ? -8.112 0.339 -10.375 1.00 92.04 17 A 1 ATOM 125 C CB . ALA A 1 17 ? -9.114 -2.237 -9.277 1.00 93.71 17 A 1 ATOM 126 O OXT . ALA A 1 17 ? -9.052 -0.442 -12.163 1.00 85.28 17 A 1 #