# 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_spkb25354 # _entry.id spkb25354 # 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" "C6 H10 N3 O2" 156.162 HIS y HISTIDINE c1c([nH+]c[nH]1)C[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" "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" "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 LYS 2 1 n VAL 3 1 n VAL 4 1 n ILE 5 1 n LEU 6 1 n MET 7 1 n ALA 8 1 n LEU 9 1 n LEU 10 1 n VAL 11 1 n LEU 12 1 n THR 13 1 n ALA 14 1 n HIS 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 @ 2025-07-08 17:43:16)" _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 96.19 _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 92.75 1 1 A LYS 2 2 94.03 1 2 A VAL 3 2 98.26 1 3 A VAL 4 2 98.43 1 4 A ILE 5 2 97.83 1 5 A LEU 6 2 96.96 1 6 A MET 7 2 95.99 1 7 A ALA 8 2 98.73 1 8 A LEU 9 2 97.77 1 9 A LEU 10 2 97.39 1 10 A VAL 11 2 98.44 1 11 A LEU 12 2 96.84 1 12 A THR 13 2 97.39 1 13 A ALA 14 2 98.36 1 14 A HIS 15 2 92.99 1 15 A CYS 16 2 89.89 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 LYS . 2 A 2 A 3 1 n VAL . 3 A 3 A 4 1 n VAL . 4 A 4 A 5 1 n ILE . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n MET . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n VAL . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n THR . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n HIS . 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 ? -0.774 11.864 0.354 1.00 97.44 1 A 1 ATOM 2 C CA . MET A 1 1 ? -1.556 10.618 0.424 1.00 97.54 1 A 1 ATOM 3 C C . MET A 1 1 ? -0.690 9.473 0.943 1.00 97.89 1 A 1 ATOM 4 O O . MET A 1 1 ? -0.090 8.738 0.164 1.00 96.85 1 A 1 ATOM 5 C CB . MET A 1 1 ? -2.087 10.246 -0.957 1.00 95.83 1 A 1 ATOM 6 C CG . MET A 1 1 ? -2.998 11.310 -1.529 1.00 90.48 1 A 1 ATOM 7 S SD . MET A 1 1 ? -3.596 10.882 -3.168 1.00 88.00 1 A 1 ATOM 8 C CE . MET A 1 1 ? -4.523 12.344 -3.564 1.00 77.98 1 A 1 ATOM 9 N N . LYS A 1 2 ? -0.614 9.335 2.257 1.00 98.45 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 0.188 8.279 2.870 1.00 98.49 2 A 1 ATOM 11 C C . LYS A 1 2 ? -0.625 7.007 3.054 1.00 98.61 2 A 1 ATOM 12 O O . LYS A 1 2 ? -0.101 5.904 2.914 1.00 98.52 2 A 1 ATOM 13 C CB . LYS A 1 2 ? 0.750 8.747 4.210 1.00 98.28 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -0.310 9.236 5.186 1.00 94.27 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -0.605 10.713 4.980 1.00 91.91 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -1.573 11.235 6.016 1.00 86.62 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -1.800 12.693 5.856 1.00 81.15 2 A 1 ATOM 18 N N . VAL A 1 3 ? -1.901 7.166 3.363 1.00 98.80 3 A 1 ATOM 19 C CA . VAL A 1 3 ? -2.783 6.020 3.566 1.00 98.81 3 A 1 ATOM 20 C C . VAL A 1 3 ? -2.899 5.194 2.292 1.00 98.85 3 A 1 ATOM 21 O O . VAL A 1 3 ? -2.858 3.962 2.321 1.00 98.71 3 A 1 ATOM 22 C CB . VAL A 1 3 ? -4.182 6.478 4.017 1.00 98.62 3 A 1 ATOM 23 C CG1 . VAL A 1 3 ? -5.086 5.278 4.219 1.00 97.00 3 A 1 ATOM 24 C CG2 . VAL A 1 3 ? -4.083 7.297 5.287 1.00 97.02 3 A 1 ATOM 25 N N . VAL A 1 4 ? -3.050 5.886 1.174 1.00 98.84 4 A 1 ATOM 26 C CA . VAL A 1 4 ? -3.170 5.224 -0.123 1.00 98.84 4 A 1 ATOM 27 C C . VAL A 1 4 ? -1.918 4.415 -0.430 1.00 98.86 4 A 1 ATOM 28 O O . VAL A 1 4 ? -1.989 3.286 -0.925 1.00 98.75 4 A 1 ATOM 29 C CB . VAL A 1 4 ? -3.413 6.250 -1.241 1.00 98.71 4 A 1 ATOM 30 C CG1 . VAL A 1 4 ? -3.515 5.558 -2.588 1.00 97.52 4 A 1 ATOM 31 C CG2 . VAL A 1 4 ? -4.673 7.047 -0.958 1.00 97.49 4 A 1 ATOM 32 N N . ILE A 1 5 ? -0.786 4.997 -0.139 1.00 98.72 5 A 1 ATOM 33 C CA . ILE A 1 5 ? 0.488 4.337 -0.387 1.00 98.67 5 A 1 ATOM 34 C C . ILE A 1 5 ? 0.610 3.073 0.452 1.00 98.70 5 A 1 ATOM 35 O O . ILE A 1 5 ? 1.046 2.026 -0.022 1.00 98.65 5 A 1 ATOM 36 C CB . ILE A 1 5 ? 1.658 5.281 -0.073 1.00 98.60 5 A 1 ATOM 37 C CG1 . ILE A 1 5 ? 1.537 6.568 -0.895 1.00 97.68 5 A 1 ATOM 38 C CG2 . ILE A 1 5 ? 2.986 4.588 -0.360 1.00 97.39 5 A 1 ATOM 39 C CD1 . ILE A 1 5 ? 1.540 6.317 -2.387 1.00 94.21 5 A 1 ATOM 40 N N . LEU A 1 6 ? 0.230 3.187 1.697 1.00 98.80 6 A 1 ATOM 41 C CA . LEU A 1 6 ? 0.295 2.053 2.609 1.00 98.77 6 A 1 ATOM 42 C C . LEU A 1 6 ? -0.614 0.926 2.142 1.00 98.82 6 A 1 ATOM 43 O O . LEU A 1 6 ? -0.239 -0.247 2.173 1.00 98.79 6 A 1 ATOM 44 C CB . LEU A 1 6 ? -0.112 2.500 4.013 1.00 98.67 6 A 1 ATOM 45 C CG . LEU A 1 6 ? 0.911 3.402 4.694 1.00 94.47 6 A 1 ATOM 46 C CD1 . LEU A 1 6 ? 0.328 3.996 5.963 1.00 93.11 6 A 1 ATOM 47 C CD2 . LEU A 1 6 ? 2.177 2.626 5.012 1.00 94.28 6 A 1 ATOM 48 N N . MET A 1 7 ? -1.797 1.291 1.721 1.00 98.70 7 A 1 ATOM 49 C CA . MET A 1 7 ? -2.756 0.307 1.232 1.00 98.68 7 A 1 ATOM 50 C C . MET A 1 7 ? -2.220 -0.398 -0.008 1.00 98.76 7 A 1 ATOM 51 O O . MET A 1 7 ? -2.287 -1.619 -0.124 1.00 98.71 7 A 1 ATOM 52 C CB . MET A 1 7 ? -4.084 0.982 0.905 1.00 98.57 7 A 1 ATOM 53 C CG . MET A 1 7 ? -4.851 1.406 2.147 1.00 96.29 7 A 1 ATOM 54 S SD . MET A 1 7 ? -6.460 2.093 1.762 1.00 92.34 7 A 1 ATOM 55 C CE . MET A 1 7 ? -7.091 2.341 3.419 1.00 85.84 7 A 1 ATOM 56 N N . ALA A 1 8 ? -1.689 0.383 -0.915 1.00 98.75 8 A 1 ATOM 57 C CA . ALA A 1 8 ? -1.134 -0.166 -2.143 1.00 98.74 8 A 1 ATOM 58 C C . ALA A 1 8 ? 0.036 -1.095 -1.841 1.00 98.80 8 A 1 ATOM 59 O O . ALA A 1 8 ? 0.170 -2.164 -2.434 1.00 98.71 8 A 1 ATOM 60 C CB . ALA A 1 8 ? -0.682 0.966 -3.053 1.00 98.64 8 A 1 ATOM 61 N N . LEU A 1 9 ? 0.861 -0.689 -0.905 1.00 98.86 9 A 1 ATOM 62 C CA . LEU A 1 9 ? 2.014 -1.484 -0.508 1.00 98.83 9 A 1 ATOM 63 C C . LEU A 1 9 ? 1.573 -2.807 0.102 1.00 98.86 9 A 1 ATOM 64 O O . LEU A 1 9 ? 2.144 -3.858 -0.184 1.00 98.77 9 A 1 ATOM 65 C CB . LEU A 1 9 ? 2.850 -0.707 0.504 1.00 98.70 9 A 1 ATOM 66 C CG . LEU A 1 9 ? 4.160 -1.392 0.868 1.00 96.61 9 A 1 ATOM 67 C CD1 . LEU A 1 9 ? 5.126 -1.335 -0.305 1.00 95.61 9 A 1 ATOM 68 C CD2 . LEU A 1 9 ? 4.782 -0.740 2.090 1.00 95.95 9 A 1 ATOM 69 N N . LEU A 1 10 ? 0.573 -2.742 0.942 1.00 98.79 10 A 1 ATOM 70 C CA . LEU A 1 10 ? 0.044 -3.931 1.598 1.00 98.76 10 A 1 ATOM 71 C C . LEU A 1 10 ? -0.483 -4.917 0.572 1.00 98.80 10 A 1 ATOM 72 O O . LEU A 1 10 ? -0.208 -6.119 0.644 1.00 98.66 10 A 1 ATOM 73 C CB . LEU A 1 10 ? -1.057 -3.533 2.581 1.00 98.65 10 A 1 ATOM 74 C CG . LEU A 1 10 ? -1.497 -4.662 3.511 1.00 96.25 10 A 1 ATOM 75 C CD1 . LEU A 1 10 ? -1.952 -4.084 4.845 1.00 94.17 10 A 1 ATOM 76 C CD2 . LEU A 1 10 ? -2.622 -5.470 2.896 1.00 95.03 10 A 1 ATOM 77 N N . VAL A 1 11 ? -1.246 -4.409 -0.383 1.00 98.88 11 A 1 ATOM 78 C CA . VAL A 1 11 ? -1.807 -5.247 -1.436 1.00 98.83 11 A 1 ATOM 79 C C . VAL A 1 11 ? -0.695 -5.864 -2.266 1.00 98.85 11 A 1 ATOM 80 O O . VAL A 1 11 ? -0.735 -7.050 -2.604 1.00 98.72 11 A 1 ATOM 81 C CB . VAL A 1 11 ? -2.740 -4.437 -2.341 1.00 98.67 11 A 1 ATOM 82 C CG1 . VAL A 1 11 ? -3.225 -5.285 -3.505 1.00 97.43 11 A 1 ATOM 83 C CG2 . VAL A 1 11 ? -3.920 -3.920 -1.542 1.00 97.73 11 A 1 ATOM 84 N N . LEU A 1 12 ? 0.290 -5.063 -2.586 1.00 98.71 12 A 1 ATOM 85 C CA . LEU A 1 12 ? 1.419 -5.529 -3.381 1.00 98.65 12 A 1 ATOM 86 C C . LEU A 1 12 ? 2.149 -6.655 -2.672 1.00 98.70 12 A 1 ATOM 87 O O . LEU A 1 12 ? 2.511 -7.660 -3.282 1.00 98.47 12 A 1 ATOM 88 C CB . LEU A 1 12 ? 2.384 -4.378 -3.634 1.00 98.47 12 A 1 ATOM 89 C CG . LEU A 1 12 ? 3.524 -4.730 -4.577 1.00 95.47 12 A 1 ATOM 90 C CD1 . LEU A 1 12 ? 2.995 -4.945 -5.982 1.00 92.68 12 A 1 ATOM 91 C CD2 . LEU A 1 12 ? 4.575 -3.639 -4.564 1.00 93.56 12 A 1 ATOM 92 N N . THR A 1 13 ? 2.359 -6.488 -1.386 1.00 98.66 13 A 1 ATOM 93 C CA . THR A 1 13 ? 3.043 -7.493 -0.583 1.00 98.54 13 A 1 ATOM 94 C C . THR A 1 13 ? 2.256 -8.792 -0.563 1.00 98.53 13 A 1 ATOM 95 O O . THR A 1 13 ? 2.827 -9.878 -0.656 1.00 97.98 13 A 1 ATOM 96 C CB . THR A 1 13 ? 3.234 -7.002 0.854 1.00 98.08 13 A 1 ATOM 97 O OG1 . THR A 1 13 ? 3.961 -5.776 0.849 1.00 94.65 13 A 1 ATOM 98 C CG2 . THR A 1 13 ? 3.997 -8.030 1.669 1.00 95.32 13 A 1 ATOM 99 N N . ALA A 1 14 ? 0.953 -8.682 -0.423 1.00 98.64 14 A 1 ATOM 100 C CA . ALA A 1 14 ? 0.085 -9.850 -0.383 1.00 98.54 14 A 1 ATOM 101 C C . ALA A 1 14 ? 0.071 -10.571 -1.722 1.00 98.51 14 A 1 ATOM 102 O O . ALA A 1 14 ? 0.052 -11.799 -1.780 1.00 97.88 14 A 1 ATOM 103 C CB . ALA A 1 14 ? -1.327 -9.443 0.004 1.00 98.23 14 A 1 ATOM 104 N N . HIS A 1 15 ? 0.078 -9.793 -2.796 1.00 98.04 15 A 1 ATOM 105 C CA . HIS A 1 15 ? 0.063 -10.361 -4.140 1.00 97.60 15 A 1 ATOM 106 C C . HIS A 1 15 ? 1.380 -11.050 -4.463 1.00 97.51 15 A 1 ATOM 107 O O . HIS A 1 15 ? 1.422 -12.254 -4.704 1.00 95.79 15 A 1 ATOM 108 C CB . HIS A 1 15 ? -0.220 -9.265 -5.172 1.00 96.91 15 A 1 ATOM 109 C CG . HIS A 1 15 ? -1.686 -8.986 -5.325 1.00 94.50 15 A 1 ATOM 110 N ND1 . HIS A 1 15 ? -2.412 -9.381 -6.414 1.00 85.97 15 A 1 ATOM 111 C CD2 . HIS A 1 15 ? -2.552 -8.348 -4.513 1.00 85.93 15 A 1 ATOM 112 C CE1 . HIS A 1 15 ? -3.669 -8.989 -6.257 1.00 88.62 15 A 1 ATOM 113 N NE2 . HIS A 1 15 ? -3.789 -8.363 -5.114 1.00 89.02 15 A 1 ATOM 114 N N . CYS A 1 16 ? 2.449 -10.267 -4.464 1.00 95.76 16 A 1 ATOM 115 C CA . CYS A 1 16 ? 3.774 -10.797 -4.777 1.00 94.09 16 A 1 ATOM 116 C C . CYS A 1 16 ? 3.754 -11.727 -5.990 1.00 93.16 16 A 1 ATOM 117 O O . CYS A 1 16 ? 4.222 -12.867 -5.908 1.00 90.60 16 A 1 ATOM 118 C CB . CYS A 1 16 ? 4.326 -11.547 -3.563 1.00 90.86 16 A 1 ATOM 119 S SG . CYS A 1 16 ? 4.923 -10.444 -2.270 1.00 84.15 16 A 1 ATOM 120 O OXT . CYS A 1 16 ? 3.245 -11.312 -7.059 1.00 80.58 16 A 1 #