# 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_spkb39207 # _entry.id spkb39207 # 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" "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" "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 ILE 2 1 n ARG 3 1 n LYS 4 1 n LEU 5 1 n ALA 6 1 n ALA 7 1 n LEU 8 1 n ILE 9 1 n VAL 10 1 n ALA 11 1 n ALA 12 1 n ALA 13 1 n ALA 14 1 n LEU 15 1 n GLN 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 06:36:26)" _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 96.00 _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 90.56 1 1 A ILE 2 2 96.53 1 2 A ARG 3 2 93.31 1 3 A LYS 4 2 94.62 1 4 A LEU 5 2 96.96 1 5 A ALA 6 2 98.66 1 6 A ALA 7 2 98.64 1 7 A LEU 8 2 97.26 1 8 A ILE 9 2 97.34 1 9 A VAL 10 2 98.26 1 10 A ALA 11 2 98.62 1 11 A ALA 12 2 98.69 1 12 A ALA 13 2 98.65 1 13 A ALA 14 2 98.66 1 14 A LEU 15 2 96.28 1 15 A GLN 16 2 93.42 1 16 A ALA 17 2 92.40 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 ILE . 2 A 2 A 3 1 n ARG . 3 A 3 A 4 1 n LYS . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n ALA . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n ILE . 9 A 9 A 10 1 n VAL . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n ALA . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n LEU . 15 A 15 A 16 1 n GLN . 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 ? -14.440 0.784 2.101 1.00 94.37 1 A 1 ATOM 2 C CA . MET A 1 1 ? -13.199 1.051 2.857 1.00 95.28 1 A 1 ATOM 3 C C . MET A 1 1 ? -12.032 1.313 1.911 1.00 96.58 1 A 1 ATOM 4 O O . MET A 1 1 ? -12.012 0.820 0.791 1.00 95.41 1 A 1 ATOM 5 C CB . MET A 1 1 ? -12.873 -0.147 3.748 1.00 91.90 1 A 1 ATOM 6 C CG . MET A 1 1 ? -13.644 -0.112 5.056 1.00 86.93 1 A 1 ATOM 7 S SD . MET A 1 1 ? -13.559 -1.688 5.907 1.00 86.17 1 A 1 ATOM 8 C CE . MET A 1 1 ? -14.574 -1.342 7.329 1.00 77.82 1 A 1 ATOM 9 N N . ILE A 1 2 ? -11.074 2.083 2.356 1.00 97.09 2 A 1 ATOM 10 C CA . ILE A 1 2 ? -9.923 2.447 1.533 1.00 97.65 2 A 1 ATOM 11 C C . ILE A 1 2 ? -8.660 1.698 1.955 1.00 98.10 2 A 1 ATOM 12 O O . ILE A 1 2 ? -7.553 2.023 1.516 1.00 97.66 2 A 1 ATOM 13 C CB . ILE A 1 2 ? -9.662 3.951 1.609 1.00 97.29 2 A 1 ATOM 14 C CG1 . ILE A 1 2 ? -10.747 4.691 2.396 1.00 95.72 2 A 1 ATOM 15 C CG2 . ILE A 1 2 ? -9.556 4.514 0.181 1.00 95.24 2 A 1 ATOM 16 C CD1 . ILE A 1 2 ? -10.208 5.914 3.070 1.00 93.45 2 A 1 ATOM 17 N N . ARG A 1 3 ? -8.832 0.718 2.804 1.00 98.40 3 A 1 ATOM 18 C CA . ARG A 1 3 ? -7.687 -0.048 3.308 1.00 98.57 3 A 1 ATOM 19 C C . ARG A 1 3 ? -6.946 -0.738 2.171 1.00 98.69 3 A 1 ATOM 20 O O . ARG A 1 3 ? -5.719 -0.812 2.170 1.00 98.46 3 A 1 ATOM 21 C CB . ARG A 1 3 ? -8.169 -1.088 4.319 1.00 98.31 3 A 1 ATOM 22 C CG . ARG A 1 3 ? -7.462 -0.949 5.656 1.00 96.04 3 A 1 ATOM 23 C CD . ARG A 1 3 ? -7.510 -2.250 6.437 1.00 93.88 3 A 1 ATOM 24 N NE . ARG A 1 3 ? -6.198 -2.562 7.008 1.00 89.91 3 A 1 ATOM 25 C CZ . ARG A 1 3 ? -5.945 -3.631 7.750 1.00 88.08 3 A 1 ATOM 26 N NH1 . ARG A 1 3 ? -6.895 -4.502 8.041 1.00 83.31 3 A 1 ATOM 27 N NH2 . ARG A 1 3 ? -4.717 -3.836 8.205 1.00 82.78 3 A 1 ATOM 28 N N . LYS A 1 4 ? -7.699 -1.217 1.199 1.00 98.50 4 A 1 ATOM 29 C CA . LYS A 1 4 ? -7.116 -1.893 0.041 1.00 98.58 4 A 1 ATOM 30 C C . LYS A 1 4 ? -6.271 -0.921 -0.774 1.00 98.65 4 A 1 ATOM 31 O O . LYS A 1 4 ? -5.139 -1.226 -1.144 1.00 98.57 4 A 1 ATOM 32 C CB . LYS A 1 4 ? -8.232 -2.479 -0.815 1.00 98.53 4 A 1 ATOM 33 C CG . LYS A 1 4 ? -7.717 -3.461 -1.846 1.00 95.02 4 A 1 ATOM 34 C CD . LYS A 1 4 ? -7.764 -4.892 -1.320 1.00 92.88 4 A 1 ATOM 35 C CE . LYS A 1 4 ? -8.050 -5.861 -2.455 1.00 88.65 4 A 1 ATOM 36 N NZ . LYS A 1 4 ? -8.358 -7.213 -1.936 1.00 82.17 4 A 1 ATOM 37 N N . LEU A 1 5 ? -6.833 0.241 -1.052 1.00 98.57 5 A 1 ATOM 38 C CA . LEU A 1 5 ? -6.129 1.261 -1.820 1.00 98.62 5 A 1 ATOM 39 C C . LEU A 1 5 ? -4.909 1.762 -1.062 1.00 98.73 5 A 1 ATOM 40 O O . LEU A 1 5 ? -3.832 1.919 -1.633 1.00 98.63 5 A 1 ATOM 41 C CB . LEU A 1 5 ? -7.077 2.419 -2.122 1.00 98.48 5 A 1 ATOM 42 C CG . LEU A 1 5 ? -6.679 3.203 -3.361 1.00 95.81 5 A 1 ATOM 43 C CD1 . LEU A 1 5 ? -7.065 2.433 -4.614 1.00 93.32 5 A 1 ATOM 44 C CD2 . LEU A 1 5 ? -7.332 4.571 -3.359 1.00 93.49 5 A 1 ATOM 45 N N . ALA A 1 6 ? -5.092 2.009 0.222 1.00 98.71 6 A 1 ATOM 46 C CA . ALA A 1 6 ? -4.002 2.491 1.065 1.00 98.70 6 A 1 ATOM 47 C C . ALA A 1 6 ? -2.862 1.479 1.108 1.00 98.74 6 A 1 ATOM 48 O O . ALA A 1 6 ? -1.689 1.846 1.075 1.00 98.61 6 A 1 ATOM 49 C CB . ALA A 1 6 ? -4.523 2.750 2.470 1.00 98.53 6 A 1 ATOM 50 N N . ALA A 1 7 ? -3.218 0.216 1.183 1.00 98.68 7 A 1 ATOM 51 C CA . ALA A 1 7 ? -2.223 -0.850 1.229 1.00 98.68 7 A 1 ATOM 52 C C . ALA A 1 7 ? -1.414 -0.894 -0.064 1.00 98.73 7 A 1 ATOM 53 O O . ALA A 1 7 ? -0.209 -1.142 -0.044 1.00 98.59 7 A 1 ATOM 54 C CB . ALA A 1 7 ? -2.917 -2.186 1.459 1.00 98.54 7 A 1 ATOM 55 N N . LEU A 1 8 ? -2.087 -0.635 -1.174 1.00 98.66 8 A 1 ATOM 56 C CA . LEU A 1 8 ? -1.422 -0.631 -2.478 1.00 98.67 8 A 1 ATOM 57 C C . LEU A 1 8 ? -0.417 0.508 -2.570 1.00 98.76 8 A 1 ATOM 58 O O . LEU A 1 8 ? 0.700 0.327 -3.056 1.00 98.67 8 A 1 ATOM 59 C CB . LEU A 1 8 ? -2.473 -0.501 -3.584 1.00 98.55 8 A 1 ATOM 60 C CG . LEU A 1 8 ? -2.777 -1.819 -4.282 1.00 96.40 8 A 1 ATOM 61 C CD1 . LEU A 1 8 ? -4.262 -1.957 -4.576 1.00 94.05 8 A 1 ATOM 62 C CD2 . LEU A 1 8 ? -1.980 -1.913 -5.578 1.00 94.32 8 A 1 ATOM 63 N N . ILE A 1 9 ? -0.819 1.665 -2.105 1.00 98.64 9 A 1 ATOM 64 C CA . ILE A 1 9 ? 0.048 2.842 -2.131 1.00 98.59 9 A 1 ATOM 65 C C . ILE A 1 9 ? 1.253 2.632 -1.225 1.00 98.69 9 A 1 ATOM 66 O O . ILE A 1 9 ? 2.388 2.936 -1.593 1.00 98.63 9 A 1 ATOM 67 C CB . ILE A 1 9 ? -0.724 4.096 -1.689 1.00 98.42 9 A 1 ATOM 68 C CG1 . ILE A 1 9 ? -2.001 4.277 -2.522 1.00 96.95 9 A 1 ATOM 69 C CG2 . ILE A 1 9 ? 0.173 5.334 -1.823 1.00 96.44 9 A 1 ATOM 70 C CD1 . ILE A 1 9 ? -1.729 4.377 -4.013 1.00 92.40 9 A 1 ATOM 71 N N . VAL A 1 10 ? 0.991 2.137 -0.038 1.00 98.77 10 A 1 ATOM 72 C CA . VAL A 1 10 ? 2.055 1.890 0.935 1.00 98.74 10 A 1 ATOM 73 C C . VAL A 1 10 ? 3.010 0.819 0.422 1.00 98.80 10 A 1 ATOM 74 O O . VAL A 1 10 ? 4.229 0.934 0.576 1.00 98.71 10 A 1 ATOM 75 C CB . VAL A 1 10 ? 1.466 1.466 2.290 1.00 98.50 10 A 1 ATOM 76 C CG1 . VAL A 1 10 ? 2.576 1.132 3.275 1.00 96.98 10 A 1 ATOM 77 C CG2 . VAL A 1 10 ? 0.588 2.572 2.856 1.00 97.32 10 A 1 ATOM 78 N N . ALA A 1 11 ? 2.449 -0.210 -0.180 1.00 98.69 11 A 1 ATOM 79 C CA . ALA A 1 11 ? 3.258 -1.302 -0.713 1.00 98.64 11 A 1 ATOM 80 C C . ALA A 1 11 ? 4.171 -0.806 -1.827 1.00 98.75 11 A 1 ATOM 81 O O . ALA A 1 11 ? 5.341 -1.185 -1.898 1.00 98.61 11 A 1 ATOM 82 C CB . ALA A 1 11 ? 2.349 -2.409 -1.237 1.00 98.39 11 A 1 ATOM 83 N N . ALA A 1 12 ? 3.638 0.042 -2.681 1.00 98.74 12 A 1 ATOM 84 C CA . ALA A 1 12 ? 4.413 0.598 -3.786 1.00 98.72 12 A 1 ATOM 85 C C . ALA A 1 12 ? 5.519 1.505 -3.270 1.00 98.81 12 A 1 ATOM 86 O O . ALA A 1 12 ? 6.643 1.485 -3.779 1.00 98.69 12 A 1 ATOM 87 C CB . ALA A 1 12 ? 3.494 1.371 -4.722 1.00 98.50 12 A 1 ATOM 88 N N . ALA A 1 13 ? 5.199 2.295 -2.262 1.00 98.74 13 A 1 ATOM 89 C CA . ALA A 1 13 ? 6.171 3.213 -1.675 1.00 98.71 13 A 1 ATOM 90 C C . ALA A 1 13 ? 7.276 2.450 -0.961 1.00 98.79 13 A 1 ATOM 91 O O . ALA A 1 13 ? 8.443 2.840 -1.005 1.00 98.59 13 A 1 ATOM 92 C CB . ALA A 1 13 ? 5.469 4.154 -0.703 1.00 98.43 13 A 1 ATOM 93 N N . ALA A 1 14 ? 6.904 1.374 -0.297 1.00 98.78 14 A 1 ATOM 94 C CA . ALA A 1 14 ? 7.872 0.555 0.429 1.00 98.74 14 A 1 ATOM 95 C C . ALA A 1 14 ? 8.788 -0.195 -0.532 1.00 98.80 14 A 1 ATOM 96 O O . ALA A 1 14 ? 9.966 -0.405 -0.240 1.00 98.53 14 A 1 ATOM 97 C CB . ALA A 1 14 ? 7.139 -0.431 1.330 1.00 98.46 14 A 1 ATOM 98 N N . LEU A 1 15 ? 8.243 -0.599 -1.658 1.00 98.45 15 A 1 ATOM 99 C CA . LEU A 1 15 ? 9.013 -1.328 -2.664 1.00 98.28 15 A 1 ATOM 100 C C . LEU A 1 15 ? 9.932 -0.404 -3.446 1.00 98.33 15 A 1 ATOM 101 O O . LEU A 1 15 ? 11.105 -0.712 -3.664 1.00 97.56 15 A 1 ATOM 102 C CB . LEU A 1 15 ? 8.062 -2.054 -3.620 1.00 97.92 15 A 1 ATOM 103 C CG . LEU A 1 15 ? 8.378 -3.537 -3.784 1.00 96.15 15 A 1 ATOM 104 C CD1 . LEU A 1 15 ? 7.763 -4.343 -2.649 1.00 92.59 15 A 1 ATOM 105 C CD2 . LEU A 1 15 ? 7.873 -4.042 -5.127 1.00 90.94 15 A 1 ATOM 106 N N . GLN A 1 16 ? 9.387 0.726 -3.871 1.00 98.24 16 A 1 ATOM 107 C CA . GLN A 1 16 ? 10.167 1.690 -4.661 1.00 98.01 16 A 1 ATOM 108 C C . GLN A 1 16 ? 10.651 2.847 -3.804 1.00 98.09 16 A 1 ATOM 109 O O . GLN A 1 16 ? 11.815 3.231 -3.870 1.00 96.69 16 A 1 ATOM 110 C CB . GLN A 1 16 ? 9.319 2.205 -5.828 1.00 97.02 16 A 1 ATOM 111 C CG . GLN A 1 16 ? 9.303 1.225 -6.991 1.00 93.34 16 A 1 ATOM 112 C CD . GLN A 1 16 ? 9.905 1.832 -8.253 1.00 90.54 16 A 1 ATOM 113 O OE1 . GLN A 1 16 ? 10.425 2.941 -8.233 1.00 84.86 16 A 1 ATOM 114 N NE2 . GLN A 1 16 ? 9.828 1.132 -9.371 1.00 84.03 16 A 1 ATOM 115 N N . ALA A 1 17 ? 9.730 3.378 -3.004 1.00 96.63 17 A 1 ATOM 116 C CA . ALA A 1 17 ? 10.031 4.513 -2.115 1.00 94.92 17 A 1 ATOM 117 C C . ALA A 1 17 ? 9.690 5.826 -2.804 1.00 93.79 17 A 1 ATOM 118 O O . ALA A 1 17 ? 9.294 6.777 -2.111 1.00 90.10 17 A 1 ATOM 119 C CB . ALA A 1 17 ? 11.504 4.497 -1.709 1.00 92.72 17 A 1 ATOM 120 O OXT . ALA A 1 17 ? 9.780 5.902 -3.998 1.00 86.26 17 A 1 #