# 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_spkb38885 # _entry.id spkb38885 # 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" "C3 H7 N O2 S" 121.158 CYS y CYSTEINE C([C@@H](C(=O)O)N)S ? "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" "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 LEU 2 1 n ARG 3 1 n VAL 4 1 n PRO 5 1 n LEU 6 1 n LEU 7 1 n VAL 8 1 n LEU 9 1 n CYS 10 1 n LEU 11 1 n ALA 12 1 n LEU 13 1 n SER 14 1 n VAL 15 1 n GLY 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 @ 2025-07-09 13:38:56)" _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 92.01 _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 82.80 1 1 A LEU 2 2 87.71 1 2 A ARG 3 2 85.57 1 3 A VAL 4 2 93.79 1 4 A PRO 5 2 95.55 1 5 A LEU 6 2 94.08 1 6 A LEU 7 2 94.50 1 7 A VAL 8 2 95.98 1 8 A LEU 9 2 94.21 1 9 A CYS 10 2 96.00 1 10 A LEU 11 2 93.72 1 11 A ALA 12 2 97.32 1 12 A LEU 13 2 94.68 1 13 A SER 14 2 94.90 1 14 A VAL 15 2 92.64 1 15 A GLY 16 2 92.45 1 16 A ALA 17 2 83.75 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 LEU . 2 A 2 A 3 1 n ARG . 3 A 3 A 4 1 n VAL . 4 A 4 A 5 1 n PRO . 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 LEU . 9 A 9 A 10 1 n CYS . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n SER . 14 A 14 A 15 1 n VAL . 15 A 15 A 16 1 n GLY . 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 ? -0.458 12.066 7.205 1.00 89.38 1 A 1 ATOM 2 C CA . MET A 1 1 ? 0.441 11.106 6.550 1.00 90.44 1 A 1 ATOM 3 C C . MET A 1 1 ? -0.183 9.706 6.512 1.00 91.82 1 A 1 ATOM 4 O O . MET A 1 1 ? 0.324 8.779 7.140 1.00 87.84 1 A 1 ATOM 5 C CB . MET A 1 1 ? 1.780 11.062 7.281 1.00 85.34 1 A 1 ATOM 6 C CG . MET A 1 1 ? 1.636 10.910 8.788 1.00 79.24 1 A 1 ATOM 7 S SD . MET A 1 1 ? 3.204 11.172 9.616 1.00 74.19 1 A 1 ATOM 8 C CE . MET A 1 1 ? 2.674 11.161 11.321 1.00 64.15 1 A 1 ATOM 9 N N . LEU A 1 2 ? -1.276 9.578 5.787 1.00 92.80 2 A 1 ATOM 10 C CA . LEU A 1 2 ? -1.984 8.311 5.661 1.00 93.48 2 A 1 ATOM 11 C C . LEU A 1 2 ? -1.798 7.712 4.269 1.00 95.29 2 A 1 ATOM 12 O O . LEU A 1 2 ? -2.415 6.702 3.932 1.00 92.64 2 A 1 ATOM 13 C CB . LEU A 1 2 ? -3.468 8.521 5.956 1.00 90.94 2 A 1 ATOM 14 C CG . LEU A 1 2 ? -4.057 7.461 6.874 1.00 83.26 2 A 1 ATOM 15 C CD1 . LEU A 1 2 ? -3.776 7.814 8.332 1.00 77.98 2 A 1 ATOM 16 C CD2 . LEU A 1 2 ? -5.552 7.336 6.642 1.00 75.31 2 A 1 ATOM 17 N N . ARG A 1 3 ? -0.952 8.351 3.493 1.00 93.72 3 A 1 ATOM 18 C CA . ARG A 1 3 ? -0.700 7.890 2.128 1.00 94.97 3 A 1 ATOM 19 C C . ARG A 1 3 ? 0.275 6.721 2.107 1.00 96.02 3 A 1 ATOM 20 O O . ARG A 1 3 ? 0.275 5.925 1.172 1.00 94.76 3 A 1 ATOM 21 C CB . ARG A 1 3 ? -0.154 9.039 1.286 1.00 93.29 3 A 1 ATOM 22 C CG . ARG A 1 3 ? -1.192 10.104 1.020 1.00 87.16 3 A 1 ATOM 23 C CD . ARG A 1 3 ? -0.693 11.061 -0.045 1.00 83.84 3 A 1 ATOM 24 N NE . ARG A 1 3 ? 0.440 11.851 0.445 1.00 78.74 3 A 1 ATOM 25 C CZ . ARG A 1 3 ? 1.315 12.458 -0.347 1.00 76.94 3 A 1 ATOM 26 N NH1 . ARG A 1 3 ? 1.203 12.375 -1.658 1.00 69.24 3 A 1 ATOM 27 N NH2 . ARG A 1 3 ? 2.308 13.145 0.181 1.00 72.64 3 A 1 ATOM 28 N N . VAL A 1 4 ? 1.089 6.648 3.131 1.00 95.57 4 A 1 ATOM 29 C CA . VAL A 1 4 ? 2.067 5.565 3.244 1.00 96.14 4 A 1 ATOM 30 C C . VAL A 1 4 ? 1.379 4.197 3.196 1.00 96.73 4 A 1 ATOM 31 O O . VAL A 1 4 ? 1.740 3.349 2.373 1.00 96.04 4 A 1 ATOM 32 C CB . VAL A 1 4 ? 2.903 5.702 4.531 1.00 94.96 4 A 1 ATOM 33 C CG1 . VAL A 1 4 ? 3.953 4.608 4.607 1.00 88.12 4 A 1 ATOM 34 C CG2 . VAL A 1 4 ? 3.569 7.067 4.593 1.00 89.00 4 A 1 ATOM 35 N N . PRO A 1 5 ? 0.401 3.989 4.074 1.00 96.23 5 A 1 ATOM 36 C CA . PRO A 1 5 ? -0.314 2.705 4.085 1.00 96.26 5 A 1 ATOM 37 C C . PRO A 1 5 ? -1.115 2.485 2.811 1.00 97.02 5 A 1 ATOM 38 O O . PRO A 1 5 ? -1.277 1.351 2.357 1.00 96.49 5 A 1 ATOM 39 C CB . PRO A 1 5 ? -1.234 2.821 5.303 1.00 94.82 5 A 1 ATOM 40 C CG . PRO A 1 5 ? -1.386 4.277 5.540 1.00 93.05 5 A 1 ATOM 41 C CD . PRO A 1 5 ? -0.082 4.897 5.110 1.00 94.97 5 A 1 ATOM 42 N N . LEU A 1 6 ? -1.604 3.572 2.251 1.00 96.42 6 A 1 ATOM 43 C CA . LEU A 1 6 ? -2.374 3.502 1.015 1.00 96.75 6 A 1 ATOM 44 C C . LEU A 1 6 ? -1.498 3.022 -0.134 1.00 97.18 6 A 1 ATOM 45 O O . LEU A 1 6 ? -1.913 2.197 -0.952 1.00 96.93 6 A 1 ATOM 46 C CB . LEU A 1 6 ? -2.958 4.879 0.699 1.00 96.56 6 A 1 ATOM 47 C CG . LEU A 1 6 ? -4.475 4.933 0.790 1.00 91.58 6 A 1 ATOM 48 C CD1 . LEU A 1 6 ? -4.952 6.336 1.112 1.00 88.34 6 A 1 ATOM 49 C CD2 . LEU A 1 6 ? -5.082 4.458 -0.526 1.00 88.85 6 A 1 ATOM 50 N N . LEU A 1 7 ? -0.288 3.547 -0.174 1.00 96.93 7 A 1 ATOM 51 C CA . LEU A 1 7 ? 0.666 3.160 -1.210 1.00 97.10 7 A 1 ATOM 52 C C . LEU A 1 7 ? 1.020 1.689 -1.078 1.00 97.49 7 A 1 ATOM 53 O O . LEU A 1 7 ? 1.089 0.960 -2.070 1.00 97.36 7 A 1 ATOM 54 C CB . LEU A 1 7 ? 1.932 4.015 -1.096 1.00 97.04 7 A 1 ATOM 55 C CG . LEU A 1 7 ? 2.717 4.110 -2.392 1.00 91.99 7 A 1 ATOM 56 C CD1 . LEU A 1 7 ? 2.873 5.567 -2.817 1.00 88.59 7 A 1 ATOM 57 C CD2 . LEU A 1 7 ? 4.077 3.463 -2.247 1.00 89.54 7 A 1 ATOM 58 N N . VAL A 1 8 ? 1.234 1.272 0.148 1.00 96.93 8 A 1 ATOM 59 C CA . VAL A 1 8 ? 1.570 -0.124 0.427 1.00 97.00 8 A 1 ATOM 60 C C . VAL A 1 8 ? 0.420 -1.030 0.001 1.00 97.16 8 A 1 ATOM 61 O O . VAL A 1 8 ? 0.638 -2.124 -0.528 1.00 96.87 8 A 1 ATOM 62 C CB . VAL A 1 8 ? 1.872 -0.318 1.922 1.00 96.51 8 A 1 ATOM 63 C CG1 . VAL A 1 8 ? 2.129 -1.781 2.243 1.00 93.61 8 A 1 ATOM 64 C CG2 . VAL A 1 8 ? 3.073 0.521 2.334 1.00 93.77 8 A 1 ATOM 65 N N . LEU A 1 9 ? -0.790 -0.562 0.245 1.00 96.61 9 A 1 ATOM 66 C CA . LEU A 1 9 ? -1.980 -1.316 -0.126 1.00 96.49 9 A 1 ATOM 67 C C . LEU A 1 9 ? -2.047 -1.495 -1.636 1.00 97.05 9 A 1 ATOM 68 O O . LEU A 1 9 ? -2.357 -2.581 -2.130 1.00 97.11 9 A 1 ATOM 69 C CB . LEU A 1 9 ? -3.231 -0.585 0.363 1.00 96.17 9 A 1 ATOM 70 C CG . LEU A 1 9 ? -4.447 -1.490 0.499 1.00 91.43 9 A 1 ATOM 71 C CD1 . LEU A 1 9 ? -4.585 -1.971 1.941 1.00 89.01 9 A 1 ATOM 72 C CD2 . LEU A 1 9 ? -5.704 -0.762 0.069 1.00 89.81 9 A 1 ATOM 73 N N . CYS A 1 10 ? -1.754 -0.428 -2.355 1.00 96.78 10 A 1 ATOM 74 C CA . CYS A 1 10 ? -1.764 -0.460 -3.812 1.00 96.76 10 A 1 ATOM 75 C C . CYS A 1 10 ? -0.741 -1.460 -4.335 1.00 97.06 10 A 1 ATOM 76 O O . CYS A 1 10 ? -1.011 -2.221 -5.263 1.00 96.55 10 A 1 ATOM 77 C CB . CYS A 1 10 ? -1.460 0.932 -4.361 1.00 96.30 10 A 1 ATOM 78 S SG . CYS A 1 10 ? -2.880 2.041 -4.259 1.00 92.55 10 A 1 ATOM 79 N N . LEU A 1 11 ? 0.423 -1.432 -3.717 1.00 96.75 11 A 1 ATOM 80 C CA . LEU A 1 11 ? 1.492 -2.348 -4.103 1.00 96.68 11 A 1 ATOM 81 C C . LEU A 1 11 ? 1.089 -3.785 -3.814 1.00 97.23 11 A 1 ATOM 82 O O . LEU A 1 11 ? 1.306 -4.681 -4.635 1.00 96.84 11 A 1 ATOM 83 C CB . LEU A 1 11 ? 2.773 -2.004 -3.339 1.00 96.20 11 A 1 ATOM 84 C CG . LEU A 1 11 ? 4.046 -2.469 -4.034 1.00 90.29 11 A 1 ATOM 85 C CD1 . LEU A 1 11 ? 4.693 -1.303 -4.781 1.00 87.62 11 A 1 ATOM 86 C CD2 . LEU A 1 11 ? 5.023 -3.054 -3.037 1.00 88.19 11 A 1 ATOM 87 N N . ALA A 1 12 ? 0.507 -3.986 -2.643 1.00 97.55 12 A 1 ATOM 88 C CA . ALA A 1 12 ? 0.057 -5.313 -2.238 1.00 97.49 12 A 1 ATOM 89 C C . ALA A 1 12 ? -0.992 -5.848 -3.206 1.00 97.75 12 A 1 ATOM 90 O O . ALA A 1 12 ? -1.005 -7.038 -3.526 1.00 97.00 12 A 1 ATOM 91 C CB . ALA A 1 12 ? -0.508 -5.253 -0.823 1.00 96.82 12 A 1 ATOM 92 N N . LEU A 1 13 ? -1.856 -4.965 -3.670 1.00 97.56 13 A 1 ATOM 93 C CA . LEU A 1 13 ? -2.904 -5.346 -4.610 1.00 97.31 13 A 1 ATOM 94 C C . LEU A 1 13 ? -2.299 -5.833 -5.917 1.00 97.52 13 A 1 ATOM 95 O O . LEU A 1 13 ? -2.784 -6.790 -6.524 1.00 96.30 13 A 1 ATOM 96 C CB . LEU A 1 13 ? -3.815 -4.147 -4.869 1.00 96.68 13 A 1 ATOM 97 C CG . LEU A 1 13 ? -4.865 -3.916 -3.781 1.00 93.61 13 A 1 ATOM 98 C CD1 . LEU A 1 13 ? -5.442 -2.517 -3.881 1.00 89.54 13 A 1 ATOM 99 C CD2 . LEU A 1 13 ? -5.973 -4.959 -3.909 1.00 88.92 13 A 1 ATOM 100 N N . SER A 1 14 ? -1.242 -5.173 -6.339 1.00 97.45 14 A 1 ATOM 101 C CA . SER A 1 14 ? -0.551 -5.542 -7.571 1.00 97.24 14 A 1 ATOM 102 C C . SER A 1 14 ? 0.142 -6.888 -7.422 1.00 97.15 14 A 1 ATOM 103 O O . SER A 1 14 ? 0.173 -7.690 -8.358 1.00 95.35 14 A 1 ATOM 104 C CB . SER A 1 14 ? 0.470 -4.467 -7.936 1.00 95.97 14 A 1 ATOM 105 O OG . SER A 1 14 ? 0.928 -4.640 -9.248 1.00 86.26 14 A 1 ATOM 106 N N . VAL A 1 15 ? 0.700 -7.113 -6.249 1.00 96.60 15 A 1 ATOM 107 C CA . VAL A 1 15 ? 1.405 -8.362 -5.968 1.00 95.93 15 A 1 ATOM 108 C C . VAL A 1 15 ? 0.433 -9.498 -5.702 1.00 96.01 15 A 1 ATOM 109 O O . VAL A 1 15 ? 0.598 -10.607 -6.224 1.00 92.40 15 A 1 ATOM 110 C CB . VAL A 1 15 ? 2.351 -8.195 -4.766 1.00 93.66 15 A 1 ATOM 111 C CG1 . VAL A 1 15 ? 3.055 -9.504 -4.451 1.00 86.44 15 A 1 ATOM 112 C CG2 . VAL A 1 15 ? 3.374 -7.107 -5.038 1.00 87.41 15 A 1 ATOM 113 N N . GLY A 1 16 ? -0.560 -9.213 -4.880 1.00 94.43 16 A 1 ATOM 114 C CA . GLY A 1 16 ? -1.558 -10.227 -4.531 1.00 93.15 16 A 1 ATOM 115 C C . GLY A 1 16 ? -2.707 -10.285 -5.515 1.00 92.86 16 A 1 ATOM 116 O O . GLY A 1 16 ? -3.420 -11.280 -5.582 1.00 89.36 16 A 1 ATOM 117 N N . ALA A 1 17 ? -2.866 -9.200 -6.283 1.00 91.78 17 A 1 ATOM 118 C CA . ALA A 1 17 ? -3.936 -9.090 -7.274 1.00 88.74 17 A 1 ATOM 119 C C . ALA A 1 17 ? -5.318 -9.030 -6.613 1.00 86.44 17 A 1 ATOM 120 O O . ALA A 1 17 ? -5.403 -8.838 -5.388 1.00 79.26 17 A 1 ATOM 121 C CB . ALA A 1 17 ? -3.854 -10.271 -8.254 1.00 82.96 17 A 1 ATOM 122 O OXT . ALA A 1 17 ? -6.329 -9.091 -7.328 1.00 73.35 17 A 1 #