# 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_spkb28474 # _entry.id spkb28474 # 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" "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" "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 GLN 2 1 n GLY 3 1 n PRO 4 1 n THR 5 1 n LEU 6 1 n ALA 7 1 n VAL 8 1 n LEU 9 1 n GLY 10 1 n ALA 11 1 n LEU 12 1 n LEU 13 1 n ALA 14 1 n VAL 15 1 n ALA 16 1 n VAL 17 1 n SER 18 # _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 @ 2025-07-12 10:49:08)" _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 94.23 _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 82.59 1 1 A GLN 2 2 84.63 1 2 A GLY 3 2 93.17 1 3 A PRO 4 2 95.09 1 4 A THR 5 2 94.99 1 5 A LEU 6 2 95.02 1 6 A ALA 7 2 97.50 1 7 A VAL 8 2 97.18 1 8 A LEU 9 2 95.61 1 9 A GLY 10 2 97.71 1 10 A ALA 11 2 98.04 1 11 A LEU 12 2 96.91 1 12 A LEU 13 2 95.51 1 13 A ALA 14 2 98.27 1 14 A VAL 15 2 97.60 1 15 A ALA 16 2 98.14 1 16 A VAL 17 2 96.58 1 17 A SER 18 2 90.51 1 18 # _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 GLN . 2 A 2 A 3 1 n GLY . 3 A 3 A 4 1 n PRO . 4 A 4 A 5 1 n THR . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n VAL . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n GLY . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n VAL . 15 A 15 A 16 1 n ALA . 16 A 16 A 17 1 n VAL . 17 A 17 A 18 1 n SER . 18 A 18 # _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 ? -15.363 0.840 1.875 1.00 87.36 1 A 1 ATOM 2 C CA . MET A 1 1 ? -14.419 1.657 1.079 1.00 88.45 1 A 1 ATOM 3 C C . MET A 1 1 ? -12.982 1.222 1.347 1.00 89.60 1 A 1 ATOM 4 O O . MET A 1 1 ? -12.524 1.274 2.476 1.00 86.99 1 A 1 ATOM 5 C CB . MET A 1 1 ? -14.578 3.122 1.457 1.00 84.51 1 A 1 ATOM 6 C CG . MET A 1 1 ? -15.926 3.654 1.013 1.00 81.53 1 A 1 ATOM 7 S SD . MET A 1 1 ? -16.100 5.414 1.297 1.00 76.55 1 A 1 ATOM 8 C CE . MET A 1 1 ? -16.919 5.390 2.871 1.00 65.69 1 A 1 ATOM 9 N N . GLN A 1 2 ? -12.283 0.784 0.324 1.00 89.72 2 A 1 ATOM 10 C CA . GLN A 1 2 ? -10.901 0.304 0.450 1.00 91.42 2 A 1 ATOM 11 C C . GLN A 1 2 ? -9.898 1.400 0.094 1.00 92.63 2 A 1 ATOM 12 O O . GLN A 1 2 ? -8.746 1.118 -0.229 1.00 89.46 2 A 1 ATOM 13 C CB . GLN A 1 2 ? -10.718 -0.897 -0.480 1.00 88.18 2 A 1 ATOM 14 C CG . GLN A 1 2 ? -11.626 -2.061 -0.110 1.00 82.84 2 A 1 ATOM 15 C CD . GLN A 1 2 ? -11.047 -2.881 1.028 1.00 80.63 2 A 1 ATOM 16 O OE1 . GLN A 1 2 ? -9.969 -2.585 1.516 1.00 74.01 2 A 1 ATOM 17 N NE2 . GLN A 1 2 ? -11.738 -3.919 1.446 1.00 72.74 2 A 1 ATOM 18 N N . GLY A 1 3 ? -10.328 2.632 0.130 1.00 91.44 3 A 1 ATOM 19 C CA . GLY A 1 3 ? -9.447 3.757 -0.188 1.00 92.77 3 A 1 ATOM 20 C C . GLY A 1 3 ? -8.209 3.806 0.690 1.00 94.70 3 A 1 ATOM 21 O O . GLY A 1 3 ? -7.097 4.000 0.200 1.00 93.79 3 A 1 ATOM 22 N N . PRO A 1 4 ? -8.376 3.630 2.003 1.00 95.61 4 A 1 ATOM 23 C CA . PRO A 1 4 ? -7.250 3.680 2.945 1.00 96.45 4 A 1 ATOM 24 C C . PRO A 1 4 ? -6.174 2.649 2.643 1.00 97.54 4 A 1 ATOM 25 O O . PRO A 1 4 ? -5.020 2.820 3.038 1.00 96.81 4 A 1 ATOM 26 C CB . PRO A 1 4 ? -7.906 3.411 4.307 1.00 94.43 4 A 1 ATOM 27 C CG . PRO A 1 4 ? -9.240 2.817 3.996 1.00 91.35 4 A 1 ATOM 28 C CD . PRO A 1 4 ? -9.648 3.410 2.679 1.00 93.47 4 A 1 ATOM 29 N N . THR A 1 5 ? -6.540 1.583 1.947 1.00 96.31 5 A 1 ATOM 30 C CA . THR A 1 5 ? -5.575 0.540 1.587 1.00 96.99 5 A 1 ATOM 31 C C . THR A 1 5 ? -4.418 1.141 0.790 1.00 97.53 5 A 1 ATOM 32 O O . THR A 1 5 ? -3.261 0.765 0.966 1.00 97.07 5 A 1 ATOM 33 C CB . THR A 1 5 ? -6.249 -0.545 0.743 1.00 96.05 5 A 1 ATOM 34 O OG1 . THR A 1 5 ? -7.382 -1.043 1.439 1.00 91.04 5 A 1 ATOM 35 C CG2 . THR A 1 5 ? -5.287 -1.690 0.482 1.00 89.95 5 A 1 ATOM 36 N N . LEU A 1 6 ? -4.732 2.081 -0.069 1.00 97.30 6 A 1 ATOM 37 C CA . LEU A 1 6 ? -3.709 2.741 -0.880 1.00 97.37 6 A 1 ATOM 38 C C . LEU A 1 6 ? -2.771 3.548 0.008 1.00 97.70 6 A 1 ATOM 39 O O . LEU A 1 6 ? -1.570 3.622 -0.244 1.00 97.48 6 A 1 ATOM 40 C CB . LEU A 1 6 ? -4.379 3.655 -1.901 1.00 96.79 6 A 1 ATOM 41 C CG . LEU A 1 6 ? -5.018 2.878 -3.047 1.00 93.19 6 A 1 ATOM 42 C CD1 . LEU A 1 6 ? -5.884 3.799 -3.885 1.00 90.66 6 A 1 ATOM 43 C CD2 . LEU A 1 6 ? -3.932 2.244 -3.909 1.00 89.66 6 A 1 ATOM 44 N N . ALA A 1 7 ? -3.325 4.146 1.048 1.00 97.37 7 A 1 ATOM 45 C CA . ALA A 1 7 ? -2.529 4.931 1.987 1.00 97.51 7 A 1 ATOM 46 C C . ALA A 1 7 ? -1.514 4.037 2.693 1.00 97.88 7 A 1 ATOM 47 O O . ALA A 1 7 ? -0.358 4.416 2.873 1.00 97.68 7 A 1 ATOM 48 C CB . ALA A 1 7 ? -3.446 5.591 3.003 1.00 97.06 7 A 1 ATOM 49 N N . VAL A 1 8 ? -1.955 2.849 3.074 1.00 97.58 8 A 1 ATOM 50 C CA . VAL A 1 8 ? -1.077 1.886 3.742 1.00 97.76 8 A 1 ATOM 51 C C . VAL A 1 8 ? 0.041 1.457 2.801 1.00 97.98 8 A 1 ATOM 52 O O . VAL A 1 8 ? 1.203 1.368 3.199 1.00 97.76 8 A 1 ATOM 53 C CB . VAL A 1 8 ? -1.874 0.651 4.187 1.00 97.40 8 A 1 ATOM 54 C CG1 . VAL A 1 8 ? -0.951 -0.381 4.817 1.00 96.04 8 A 1 ATOM 55 C CG2 . VAL A 1 8 ? -2.957 1.063 5.176 1.00 95.74 8 A 1 ATOM 56 N N . LEU A 1 9 ? -0.321 1.191 1.562 1.00 97.49 9 A 1 ATOM 57 C CA . LEU A 1 9 ? 0.661 0.782 0.561 1.00 97.45 9 A 1 ATOM 58 C C . LEU A 1 9 ? 1.703 1.880 0.362 1.00 97.80 9 A 1 ATOM 59 O O . LEU A 1 9 ? 2.896 1.613 0.252 1.00 97.78 9 A 1 ATOM 60 C CB . LEU A 1 9 ? -0.041 0.482 -0.763 1.00 96.95 9 A 1 ATOM 61 C CG . LEU A 1 9 ? 0.110 -0.978 -1.179 1.00 93.56 9 A 1 ATOM 62 C CD1 . LEU A 1 9 ? -0.822 -1.859 -0.356 1.00 92.24 9 A 1 ATOM 63 C CD2 . LEU A 1 9 ? -0.179 -1.140 -2.660 1.00 91.58 9 A 1 ATOM 64 N N . GLY A 1 10 ? 1.233 3.106 0.323 1.00 97.40 10 A 1 ATOM 65 C CA . GLY A 1 10 ? 2.134 4.245 0.154 1.00 97.45 10 A 1 ATOM 66 C C . GLY A 1 10 ? 3.110 4.345 1.312 1.00 97.99 10 A 1 ATOM 67 O O . GLY A 1 10 ? 4.294 4.624 1.124 1.00 97.99 10 A 1 ATOM 68 N N . ALA A 1 11 ? 2.609 4.108 2.513 1.00 98.08 11 A 1 ATOM 69 C CA . ALA A 1 11 ? 3.450 4.147 3.709 1.00 98.15 11 A 1 ATOM 70 C C . ALA A 1 11 ? 4.529 3.072 3.633 1.00 98.36 11 A 1 ATOM 71 O O . ALA A 1 11 ? 5.682 3.312 3.991 1.00 97.82 11 A 1 ATOM 72 C CB . ALA A 1 11 ? 2.586 3.939 4.943 1.00 97.78 11 A 1 ATOM 73 N N . LEU A 1 12 ? 4.141 1.897 3.161 1.00 98.08 12 A 1 ATOM 74 C CA . LEU A 1 12 ? 5.089 0.792 3.015 1.00 97.97 12 A 1 ATOM 75 C C . LEU A 1 12 ? 6.192 1.169 2.037 1.00 98.20 12 A 1 ATOM 76 O O . LEU A 1 12 ? 7.366 0.862 2.255 1.00 97.98 12 A 1 ATOM 77 C CB . LEU A 1 12 ? 4.347 -0.452 2.514 1.00 97.61 12 A 1 ATOM 78 C CG . LEU A 1 12 ? 3.853 -1.338 3.658 1.00 96.20 12 A 1 ATOM 79 C CD1 . LEU A 1 12 ? 2.789 -2.307 3.172 1.00 94.73 12 A 1 ATOM 80 C CD2 . LEU A 1 12 ? 5.026 -2.107 4.259 1.00 94.48 12 A 1 ATOM 81 N N . LEU A 1 13 ? 5.806 1.826 0.970 1.00 97.86 13 A 1 ATOM 82 C CA . LEU A 1 13 ? 6.762 2.262 -0.043 1.00 97.83 13 A 1 ATOM 83 C C . LEU A 1 13 ? 7.776 3.220 0.576 1.00 98.14 13 A 1 ATOM 84 O O . LEU A 1 13 ? 8.978 3.125 0.335 1.00 98.00 13 A 1 ATOM 85 C CB . LEU A 1 13 ? 6.008 2.945 -1.194 1.00 97.32 13 A 1 ATOM 86 C CG . LEU A 1 13 ? 6.212 2.262 -2.544 1.00 92.64 13 A 1 ATOM 87 C CD1 . LEU A 1 13 ? 7.666 2.318 -2.956 1.00 91.12 13 A 1 ATOM 88 C CD2 . LEU A 1 13 ? 5.728 0.824 -2.471 1.00 91.16 13 A 1 ATOM 89 N N . ALA A 1 14 ? 7.278 4.143 1.383 1.00 98.42 14 A 1 ATOM 90 C CA . ALA A 1 14 ? 8.145 5.115 2.048 1.00 98.38 14 A 1 ATOM 91 C C . ALA A 1 14 ? 9.134 4.408 2.974 1.00 98.46 14 A 1 ATOM 92 O O . ALA A 1 14 ? 10.305 4.784 3.048 1.00 98.04 14 A 1 ATOM 93 C CB . ALA A 1 14 ? 7.289 6.095 2.838 1.00 98.04 14 A 1 ATOM 94 N N . VAL A 1 15 ? 8.658 3.389 3.673 1.00 98.49 15 A 1 ATOM 95 C CA . VAL A 1 15 ? 9.518 2.618 4.579 1.00 98.40 15 A 1 ATOM 96 C C . VAL A 1 15 ? 10.603 1.895 3.794 1.00 98.50 15 A 1 ATOM 97 O O . VAL A 1 15 ? 11.763 1.857 4.209 1.00 98.10 15 A 1 ATOM 98 C CB . VAL A 1 15 ? 8.689 1.598 5.373 1.00 97.85 15 A 1 ATOM 99 C CG1 . VAL A 1 15 ? 9.598 0.719 6.226 1.00 95.82 15 A 1 ATOM 100 C CG2 . VAL A 1 15 ? 7.686 2.315 6.260 1.00 96.03 15 A 1 ATOM 101 N N . ALA A 1 16 ? 10.228 1.319 2.666 1.00 98.35 16 A 1 ATOM 102 C CA . ALA A 1 16 ? 11.181 0.592 1.826 1.00 98.31 16 A 1 ATOM 103 C C . ALA A 1 16 ? 12.261 1.534 1.303 1.00 98.36 16 A 1 ATOM 104 O O . ALA A 1 16 ? 13.427 1.156 1.185 1.00 97.78 16 A 1 ATOM 105 C CB . ALA A 1 16 ? 10.444 -0.059 0.661 1.00 97.88 16 A 1 ATOM 106 N N . VAL A 1 17 ? 11.869 2.748 0.992 1.00 98.38 17 A 1 ATOM 107 C CA . VAL A 1 17 ? 12.809 3.753 0.488 1.00 98.18 17 A 1 ATOM 108 C C . VAL A 1 17 ? 13.761 4.207 1.585 1.00 98.16 17 A 1 ATOM 109 O O . VAL A 1 17 ? 14.934 4.492 1.320 1.00 97.25 17 A 1 ATOM 110 C CB . VAL A 1 17 ? 12.045 4.964 -0.063 1.00 97.35 17 A 1 ATOM 111 C CG1 . VAL A 1 17 ? 13.013 6.080 -0.445 1.00 93.26 17 A 1 ATOM 112 C CG2 . VAL A 1 17 ? 11.224 4.554 -1.276 1.00 93.49 17 A 1 ATOM 113 N N . SER A 1 18 ? 13.248 4.270 2.811 1.00 96.52 18 A 1 ATOM 114 C CA . SER A 1 18 ? 14.049 4.715 3.954 1.00 95.52 18 A 1 ATOM 115 C C . SER A 1 18 ? 15.276 3.826 4.121 1.00 93.00 18 A 1 ATOM 116 O O . SER A 1 18 ? 16.332 4.333 4.521 1.00 86.31 18 A 1 ATOM 117 C CB . SER A 1 18 ? 13.209 4.663 5.234 1.00 92.32 18 A 1 ATOM 118 O OG . SER A 1 18 ? 13.007 3.338 5.652 1.00 84.27 18 A 1 ATOM 119 O OXT . SER A 1 18 ? 15.172 2.626 3.852 1.00 85.64 18 A 1 #