# 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_spkb16833 # _entry.id spkb16833 # 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" "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" "C9 H11 N O2" 165.189 PHE y PHENYLALANINE c1ccc(cc1)C[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 THR 2 1 n VAL 3 1 n ALA 4 1 n VAL 5 1 n PHE 6 1 n LEU 7 1 n ALA 8 1 n ILE 9 1 n LEU 10 1 n CYS 11 1 n LEU 12 1 n ARG 13 1 n ALA 14 1 n ALA 15 1 n LEU 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 @ 2025-07-03 22:01:05)" _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 94.20 _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 84.59 1 1 A THR 2 2 92.23 1 2 A VAL 3 2 96.04 1 3 A ALA 4 2 97.66 1 4 A VAL 5 2 96.88 1 5 A PHE 6 2 95.53 1 6 A LEU 7 2 95.64 1 7 A ALA 8 2 97.74 1 8 A ILE 9 2 95.73 1 9 A LEU 10 2 96.01 1 10 A CYS 11 2 96.89 1 11 A LEU 12 2 95.45 1 12 A ARG 13 2 89.78 1 13 A ALA 14 2 97.69 1 14 A ALA 15 2 97.56 1 15 A LEU 16 2 93.23 1 16 A ALA 17 2 88.60 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 THR . 2 A 2 A 3 1 n VAL . 3 A 3 A 4 1 n ALA . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n PHE . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n ILE . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n CYS . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n ARG . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n LEU . 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 ? -4.830 -2.171 13.311 1.00 91.07 1 A 1 ATOM 2 C CA . MET A 1 1 ? -4.167 -1.350 12.295 1.00 90.89 1 A 1 ATOM 3 C C . MET A 1 1 ? -3.749 -2.204 11.100 1.00 92.54 1 A 1 ATOM 4 O O . MET A 1 1 ? -2.852 -1.844 10.349 1.00 89.65 1 A 1 ATOM 5 C CB . MET A 1 1 ? -2.941 -0.656 12.891 1.00 86.98 1 A 1 ATOM 6 C CG . MET A 1 1 ? -3.284 0.297 14.024 1.00 80.41 1 A 1 ATOM 7 S SD . MET A 1 1 ? -1.818 1.048 14.742 1.00 77.64 1 A 1 ATOM 8 C CE . MET A 1 1 ? -2.563 2.033 16.032 1.00 67.55 1 A 1 ATOM 9 N N . THR A 1 2 ? -4.423 -3.321 10.954 1.00 93.91 2 A 1 ATOM 10 C CA . THR A 1 2 ? -4.121 -4.229 9.858 1.00 95.71 2 A 1 ATOM 11 C C . THR A 1 2 ? -4.564 -3.640 8.525 1.00 96.81 2 A 1 ATOM 12 O O . THR A 1 2 ? -3.846 -3.707 7.527 1.00 95.37 2 A 1 ATOM 13 C CB . THR A 1 2 ? -4.813 -5.577 10.073 1.00 93.16 2 A 1 ATOM 14 O OG1 . THR A 1 2 ? -4.924 -5.855 11.466 1.00 85.04 2 A 1 ATOM 15 C CG2 . THR A 1 2 ? -4.049 -6.680 9.388 1.00 85.64 2 A 1 ATOM 16 N N . VAL A 1 3 ? -5.739 -3.069 8.528 1.00 97.25 3 A 1 ATOM 17 C CA . VAL A 1 3 ? -6.293 -2.449 7.328 1.00 97.47 3 A 1 ATOM 18 C C . VAL A 1 3 ? -5.468 -1.239 6.915 1.00 97.88 3 A 1 ATOM 19 O O . VAL A 1 3 ? -5.332 -0.939 5.728 1.00 97.48 3 A 1 ATOM 20 C CB . VAL A 1 3 ? -7.754 -2.033 7.554 1.00 96.70 3 A 1 ATOM 21 C CG1 . VAL A 1 3 ? -8.353 -1.463 6.280 1.00 92.66 3 A 1 ATOM 22 C CG2 . VAL A 1 3 ? -8.573 -3.212 8.045 1.00 92.87 3 A 1 ATOM 23 N N . ALA A 1 4 ? -4.921 -0.564 7.912 1.00 97.47 4 A 1 ATOM 24 C CA . ALA A 1 4 ? -4.104 0.620 7.660 1.00 97.78 4 A 1 ATOM 25 C C . ALA A 1 4 ? -2.874 0.271 6.833 1.00 98.06 4 A 1 ATOM 26 O O . ALA A 1 4 ? -2.496 1.009 5.924 1.00 97.61 4 A 1 ATOM 27 C CB . ALA A 1 4 ? -3.686 1.257 8.979 1.00 97.36 4 A 1 ATOM 28 N N . VAL A 1 5 ? -2.262 -0.863 7.151 1.00 97.81 5 A 1 ATOM 29 C CA . VAL A 1 5 ? -1.077 -1.331 6.431 1.00 97.83 5 A 1 ATOM 30 C C . VAL A 1 5 ? -1.430 -1.661 4.989 1.00 97.99 5 A 1 ATOM 31 O O . VAL A 1 5 ? -0.724 -1.270 4.056 1.00 97.62 5 A 1 ATOM 32 C CB . VAL A 1 5 ? -0.469 -2.563 7.119 1.00 97.46 5 A 1 ATOM 33 C CG1 . VAL A 1 5 ? 0.755 -3.052 6.362 1.00 94.80 5 A 1 ATOM 34 C CG2 . VAL A 1 5 ? -0.105 -2.247 8.557 1.00 94.68 5 A 1 ATOM 35 N N . PHE A 1 6 ? -2.529 -2.368 4.819 1.00 97.49 6 A 1 ATOM 36 C CA . PHE A 1 6 ? -2.984 -2.748 3.492 1.00 97.39 6 A 1 ATOM 37 C C . PHE A 1 6 ? -3.381 -1.519 2.684 1.00 97.64 6 A 1 ATOM 38 O O . PHE A 1 6 ? -3.126 -1.439 1.483 1.00 97.49 6 A 1 ATOM 39 C CB . PHE A 1 6 ? -4.165 -3.706 3.619 1.00 97.31 6 A 1 ATOM 40 C CG . PHE A 1 6 ? -4.213 -4.716 2.507 1.00 95.91 6 A 1 ATOM 41 C CD1 . PHE A 1 6 ? -3.441 -5.864 2.569 1.00 93.79 6 A 1 ATOM 42 C CD2 . PHE A 1 6 ? -5.026 -4.512 1.408 1.00 94.02 6 A 1 ATOM 43 C CE1 . PHE A 1 6 ? -3.480 -6.794 1.547 1.00 93.19 6 A 1 ATOM 44 C CE2 . PHE A 1 6 ? -5.065 -5.440 0.380 1.00 93.04 6 A 1 ATOM 45 C CZ . PHE A 1 6 ? -4.292 -6.581 0.448 1.00 93.53 6 A 1 ATOM 46 N N . LEU A 1 7 ? -4.001 -0.583 3.365 1.00 97.67 7 A 1 ATOM 47 C CA . LEU A 1 7 ? -4.433 0.659 2.729 1.00 97.52 7 A 1 ATOM 48 C C . LEU A 1 7 ? -3.233 1.471 2.265 1.00 97.75 7 A 1 ATOM 49 O O . LEU A 1 7 ? -3.242 2.054 1.181 1.00 97.73 7 A 1 ATOM 50 C CB . LEU A 1 7 ? -5.283 1.468 3.714 1.00 97.31 7 A 1 ATOM 51 C CG . LEU A 1 7 ? -6.507 2.130 3.087 1.00 93.12 7 A 1 ATOM 52 C CD1 . LEU A 1 7 ? -7.580 2.375 4.134 1.00 91.83 7 A 1 ATOM 53 C CD2 . LEU A 1 7 ? -6.128 3.431 2.412 1.00 92.17 7 A 1 ATOM 54 N N . ALA A 1 8 ? -2.196 1.491 3.097 1.00 97.81 8 A 1 ATOM 55 C CA . ALA A 1 8 ? -0.978 2.224 2.774 1.00 97.78 8 A 1 ATOM 56 C C . ALA A 1 8 ? -0.299 1.636 1.541 1.00 97.95 8 A 1 ATOM 57 O O . ALA A 1 8 ? 0.109 2.368 0.638 1.00 97.57 8 A 1 ATOM 58 C CB . ALA A 1 8 ? -0.026 2.201 3.963 1.00 97.59 8 A 1 ATOM 59 N N . ILE A 1 9 ? -0.193 0.317 1.508 1.00 97.63 9 A 1 ATOM 60 C CA . ILE A 1 9 ? 0.427 -0.379 0.385 1.00 97.21 9 A 1 ATOM 61 C C . ILE A 1 9 ? -0.414 -0.211 -0.873 1.00 97.26 9 A 1 ATOM 62 O O . ILE A 1 9 ? 0.115 -0.031 -1.974 1.00 96.82 9 A 1 ATOM 63 C CB . ILE A 1 9 ? 0.613 -1.876 0.706 1.00 97.08 9 A 1 ATOM 64 C CG1 . ILE A 1 9 ? 1.557 -2.059 1.894 1.00 95.02 9 A 1 ATOM 65 C CG2 . ILE A 1 9 ? 1.170 -2.615 -0.513 1.00 94.67 9 A 1 ATOM 66 C CD1 . ILE A 1 9 ? 1.461 -3.433 2.521 1.00 90.19 9 A 1 ATOM 67 N N . LEU A 1 10 ? -1.712 -0.271 -0.694 1.00 97.73 10 A 1 ATOM 68 C CA . LEU A 1 10 ? -2.639 -0.110 -1.805 1.00 97.54 10 A 1 ATOM 69 C C . LEU A 1 10 ? -2.503 1.273 -2.425 1.00 97.65 10 A 1 ATOM 70 O O . LEU A 1 10 ? -2.531 1.423 -3.646 1.00 97.43 10 A 1 ATOM 71 C CB . LEU A 1 10 ? -4.076 -0.327 -1.321 1.00 97.36 10 A 1 ATOM 72 C CG . LEU A 1 10 ? -5.086 -0.527 -2.441 1.00 94.69 10 A 1 ATOM 73 C CD1 . LEU A 1 10 ? -5.038 -1.957 -2.963 1.00 92.87 10 A 1 ATOM 74 C CD2 . LEU A 1 10 ? -6.484 -0.187 -1.966 1.00 92.79 10 A 1 ATOM 75 N N . CYS A 1 11 ? -2.361 2.265 -1.579 1.00 97.90 11 A 1 ATOM 76 C CA . CYS A 1 11 ? -2.214 3.646 -2.026 1.00 97.84 11 A 1 ATOM 77 C C . CYS A 1 11 ? -0.913 3.826 -2.797 1.00 97.72 11 A 1 ATOM 78 O O . CYS A 1 11 ? -0.877 4.479 -3.836 1.00 96.99 11 A 1 ATOM 79 C CB . CYS A 1 11 ? -2.258 4.595 -0.825 1.00 97.55 11 A 1 ATOM 80 S SG . CYS A 1 11 ? -2.709 6.285 -1.278 1.00 93.32 11 A 1 ATOM 81 N N . LEU A 1 12 ? 0.154 3.229 -2.272 1.00 97.81 12 A 1 ATOM 82 C CA . LEU A 1 12 ? 1.463 3.317 -2.906 1.00 97.61 12 A 1 ATOM 83 C C . LEU A 1 12 ? 1.466 2.586 -4.240 1.00 97.62 12 A 1 ATOM 84 O O . LEU A 1 12 ? 2.031 3.072 -5.222 1.00 97.00 12 A 1 ATOM 85 C CB . LEU A 1 12 ? 2.528 2.732 -1.980 1.00 97.41 12 A 1 ATOM 86 C CG . LEU A 1 12 ? 3.964 3.035 -2.389 1.00 93.95 12 A 1 ATOM 87 C CD1 . LEU A 1 12 ? 4.316 4.478 -2.052 1.00 91.25 12 A 1 ATOM 88 C CD2 . LEU A 1 12 ? 4.929 2.086 -1.708 1.00 90.96 12 A 1 ATOM 89 N N . ARG A 1 13 ? 0.831 1.432 -4.283 1.00 97.63 13 A 1 ATOM 90 C CA . ARG A 1 13 ? 0.759 0.630 -5.492 1.00 97.48 13 A 1 ATOM 91 C C . ARG A 1 13 ? -0.066 1.332 -6.558 1.00 97.70 13 A 1 ATOM 92 O O . ARG A 1 13 ? 0.308 1.360 -7.729 1.00 97.00 13 A 1 ATOM 93 C CB . ARG A 1 13 ? 0.163 -0.741 -5.179 1.00 96.68 13 A 1 ATOM 94 C CG . ARG A 1 13 ? 0.511 -1.764 -6.237 1.00 90.61 13 A 1 ATOM 95 C CD . ARG A 1 13 ? 0.059 -3.153 -5.825 1.00 88.84 13 A 1 ATOM 96 N NE . ARG A 1 13 ? -1.395 -3.281 -5.936 1.00 85.66 13 A 1 ATOM 97 C CZ . ARG A 1 13 ? -2.034 -4.447 -5.846 1.00 82.56 13 A 1 ATOM 98 N NH1 . ARG A 1 13 ? -1.377 -5.574 -5.640 1.00 76.26 13 A 1 ATOM 99 N NH2 . ARG A 1 13 ? -3.356 -4.473 -5.962 1.00 77.21 13 A 1 ATOM 100 N N . ALA A 1 14 ? -1.175 1.890 -6.137 1.00 97.93 14 A 1 ATOM 101 C CA . ALA A 1 14 ? -2.056 2.612 -7.045 1.00 97.89 14 A 1 ATOM 102 C C . ALA A 1 14 ? -1.392 3.880 -7.560 1.00 98.09 14 A 1 ATOM 103 O O . ALA A 1 14 ? -1.700 4.353 -8.653 1.00 97.38 14 A 1 ATOM 104 C CB . ALA A 1 14 ? -3.362 2.960 -6.339 1.00 97.18 14 A 1 ATOM 105 N N . ALA A 1 15 ? -0.478 4.413 -6.759 1.00 98.00 15 A 1 ATOM 106 C CA . ALA A 1 15 ? 0.232 5.630 -7.135 1.00 97.80 15 A 1 ATOM 107 C C . ALA A 1 15 ? 1.213 5.371 -8.267 1.00 97.93 15 A 1 ATOM 108 O O . ALA A 1 15 ? 1.309 6.157 -9.210 1.00 96.90 15 A 1 ATOM 109 C CB . ALA A 1 15 ? 0.959 6.206 -5.929 1.00 97.19 15 A 1 ATOM 110 N N . LEU A 1 16 ? 1.946 4.255 -8.167 1.00 96.69 16 A 1 ATOM 111 C CA . LEU A 1 16 ? 2.935 3.922 -9.184 1.00 96.21 16 A 1 ATOM 112 C C . LEU A 1 16 ? 3.048 2.418 -9.383 1.00 96.27 16 A 1 ATOM 113 O O . LEU A 1 16 ? 2.453 1.859 -10.298 1.00 94.37 16 A 1 ATOM 114 C CB . LEU A 1 16 ? 4.291 4.512 -8.792 1.00 95.37 16 A 1 ATOM 115 C CG . LEU A 1 16 ? 5.047 5.173 -9.937 1.00 92.59 16 A 1 ATOM 116 C CD1 . LEU A 1 16 ? 6.028 6.194 -9.414 1.00 88.20 16 A 1 ATOM 117 C CD2 . LEU A 1 16 ? 5.735 4.137 -10.790 1.00 86.17 16 A 1 ATOM 118 N N . ALA A 1 17 ? 3.826 1.775 -8.504 1.00 94.51 17 A 1 ATOM 119 C CA . ALA A 1 17 ? 4.075 0.334 -8.575 1.00 92.23 17 A 1 ATOM 120 C C . ALA A 1 17 ? 2.779 -0.450 -8.424 1.00 90.25 17 A 1 ATOM 121 O O . ALA A 1 17 ? 2.438 -0.833 -7.295 1.00 86.26 17 A 1 ATOM 122 C CB . ALA A 1 17 ? 5.076 -0.089 -7.518 1.00 88.10 17 A 1 ATOM 123 O OXT . ALA A 1 17 ? 2.105 -0.683 -9.434 1.00 80.27 17 A 1 #