# 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_spkb28112 # _entry.id spkb28112 # 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 S" 121.158 CYS y CYSTEINE C([C@@H](C(=O)O)N)S ? "L-PEPTIDE LINKING" "C5 H9 N O4" 147.129 GLU y "GLUTAMIC ACID" C(CC(=O)O)[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 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" "C3 H7 N O3" 105.093 SER y SERINE C([C@@H](C(=O)O)N)O ? "L-PEPTIDE LINKING" "C11 H12 N2 O2" 204.225 TRP y TRYPTOPHAN c1ccc2c(c1)c(c[nH]2)C[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 LYS 2 1 n TRP 3 1 n LEU 4 1 n VAL 5 1 n LEU 6 1 n LEU 7 1 n GLY 8 1 n LEU 9 1 n VAL 10 1 n SER 11 1 n ILE 12 1 n SER 13 1 n GLU 14 1 n CYS 15 # _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 20:22:25)" _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 92.26 _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 89.17 1 1 A LYS 2 2 88.47 1 2 A TRP 3 2 91.36 1 3 A LEU 4 2 94.98 1 4 A VAL 5 2 96.41 1 5 A LEU 6 2 94.55 1 6 A LEU 7 2 95.01 1 7 A GLY 8 2 96.85 1 8 A LEU 9 2 93.65 1 9 A VAL 10 2 95.96 1 10 A SER 11 2 95.67 1 11 A ILE 12 2 93.20 1 12 A SER 13 2 93.30 1 13 A GLU 14 2 84.77 1 14 A CYS 15 2 86.21 1 15 # _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 TRP . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n VAL . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n GLY . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n VAL . 10 A 10 A 11 1 n SER . 11 A 11 A 12 1 n ILE . 12 A 12 A 13 1 n SER . 13 A 13 A 14 1 n GLU . 14 A 14 A 15 1 n CYS . 15 A 15 # _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 ? -3.678 1.681 13.232 1.00 94.24 1 A 1 ATOM 2 C CA . MET A 1 1 ? -3.397 2.649 12.151 1.00 94.81 1 A 1 ATOM 3 C C . MET A 1 1 ? -3.831 2.085 10.803 1.00 95.42 1 A 1 ATOM 4 O O . MET A 1 1 ? -3.531 0.939 10.485 1.00 93.32 1 A 1 ATOM 5 C CB . MET A 1 1 ? -1.903 2.974 12.099 1.00 91.46 1 A 1 ATOM 6 C CG . MET A 1 1 ? -1.389 3.580 13.392 1.00 86.59 1 A 1 ATOM 7 S SD . MET A 1 1 ? 0.376 3.922 13.343 1.00 84.24 1 A 1 ATOM 8 C CE . MET A 1 1 ? 0.625 4.605 14.965 1.00 73.25 1 A 1 ATOM 9 N N . LYS A 1 2 ? -4.542 2.886 10.015 1.00 95.34 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -5.031 2.461 8.707 1.00 95.70 2 A 1 ATOM 11 C C . LYS A 1 2 ? -4.288 3.161 7.569 1.00 96.25 2 A 1 ATOM 12 O O . LYS A 1 2 ? -4.147 2.609 6.483 1.00 95.93 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -6.530 2.750 8.592 1.00 94.64 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -7.377 1.956 9.565 1.00 88.09 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -8.842 2.351 9.458 1.00 84.51 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -9.700 1.537 10.414 1.00 76.92 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -9.786 0.117 9.996 1.00 68.82 2 A 1 ATOM 18 N N . TRP A 1 3 ? -3.813 4.369 7.824 1.00 95.35 3 A 1 ATOM 19 C CA . TRP A 1 3 ? -3.103 5.148 6.812 1.00 96.45 3 A 1 ATOM 20 C C . TRP A 1 3 ? -1.832 4.436 6.345 1.00 97.18 3 A 1 ATOM 21 O O . TRP A 1 3 ? -1.433 4.557 5.189 1.00 96.19 3 A 1 ATOM 22 C CB . TRP A 1 3 ? -2.755 6.527 7.361 1.00 95.85 3 A 1 ATOM 23 C CG . TRP A 1 3 ? -1.855 6.493 8.554 1.00 93.15 3 A 1 ATOM 24 C CD1 . TRP A 1 3 ? -2.179 6.092 9.801 1.00 89.40 3 A 1 ATOM 25 C CD2 . TRP A 1 3 ? -0.466 6.872 8.597 1.00 92.21 3 A 1 ATOM 26 N NE1 . TRP A 1 3 ? -1.085 6.188 10.629 1.00 87.50 3 A 1 ATOM 27 C CE2 . TRP A 1 3 ? -0.021 6.670 9.912 1.00 91.27 3 A 1 ATOM 28 C CE3 . TRP A 1 3 ? 0.424 7.369 7.647 1.00 88.41 3 A 1 ATOM 29 C CZ2 . TRP A 1 3 ? 1.295 6.950 10.292 1.00 88.13 3 A 1 ATOM 30 C CZ3 . TRP A 1 3 ? 1.733 7.649 8.029 1.00 84.25 3 A 1 ATOM 31 C CH2 . TRP A 1 3 ? 2.154 7.430 9.344 1.00 83.73 3 A 1 ATOM 32 N N . LEU A 1 4 ? -1.210 3.682 7.230 1.00 97.41 4 A 1 ATOM 33 C CA . LEU A 1 4 ? 0.008 2.951 6.895 1.00 97.74 4 A 1 ATOM 34 C C . LEU A 1 4 ? -0.257 1.913 5.816 1.00 98.06 4 A 1 ATOM 35 O O . LEU A 1 4 ? 0.608 1.630 4.988 1.00 97.84 4 A 1 ATOM 36 C CB . LEU A 1 4 ? 0.574 2.270 8.143 1.00 97.56 4 A 1 ATOM 37 C CG . LEU A 1 4 ? 1.127 3.230 9.194 1.00 93.59 4 A 1 ATOM 38 C CD1 . LEU A 1 4 ? 1.607 2.451 10.413 1.00 89.01 4 A 1 ATOM 39 C CD2 . LEU A 1 4 ? 2.267 4.053 8.618 1.00 88.62 4 A 1 ATOM 40 N N . VAL A 1 5 ? -1.462 1.345 5.818 1.00 97.59 5 A 1 ATOM 41 C CA . VAL A 1 5 ? -1.844 0.342 4.828 1.00 97.60 5 A 1 ATOM 42 C C . VAL A 1 5 ? -1.869 0.961 3.433 1.00 97.78 5 A 1 ATOM 43 O O . VAL A 1 5 ? -1.448 0.339 2.454 1.00 97.42 5 A 1 ATOM 44 C CB . VAL A 1 5 ? -3.221 -0.260 5.146 1.00 96.99 5 A 1 ATOM 45 C CG1 . VAL A 1 5 ? -3.598 -1.308 4.114 1.00 93.55 5 A 1 ATOM 46 C CG2 . VAL A 1 5 ? -3.222 -0.862 6.539 1.00 93.93 5 A 1 ATOM 47 N N . LEU A 1 6 ? -2.362 2.179 3.352 1.00 97.52 6 A 1 ATOM 48 C CA . LEU A 1 6 ? -2.448 2.883 2.077 1.00 97.54 6 A 1 ATOM 49 C C . LEU A 1 6 ? -1.055 3.210 1.551 1.00 97.71 6 A 1 ATOM 50 O O . LEU A 1 6 ? -0.777 3.058 0.363 1.00 97.61 6 A 1 ATOM 51 C CB . LEU A 1 6 ? -3.253 4.174 2.240 1.00 97.37 6 A 1 ATOM 52 C CG . LEU A 1 6 ? -4.676 3.978 2.756 1.00 91.16 6 A 1 ATOM 53 C CD1 . LEU A 1 6 ? -5.362 5.328 2.923 1.00 88.31 6 A 1 ATOM 54 C CD2 . LEU A 1 6 ? -5.472 3.094 1.811 1.00 89.18 6 A 1 ATOM 55 N N . LEU A 1 7 ? -0.175 3.652 2.430 1.00 97.70 7 A 1 ATOM 56 C CA . LEU A 1 7 ? 1.194 3.986 2.048 1.00 97.45 7 A 1 ATOM 57 C C . LEU A 1 7 ? 1.947 2.742 1.597 1.00 97.71 7 A 1 ATOM 58 O O . LEU A 1 7 ? 2.799 2.810 0.710 1.00 97.34 7 A 1 ATOM 59 C CB . LEU A 1 7 ? 1.922 4.631 3.226 1.00 97.04 7 A 1 ATOM 60 C CG . LEU A 1 7 ? 1.332 5.960 3.688 1.00 92.98 7 A 1 ATOM 61 C CD1 . LEU A 1 7 ? 2.089 6.463 4.913 1.00 89.75 7 A 1 ATOM 62 C CD2 . LEU A 1 7 ? 1.390 6.989 2.574 1.00 90.08 7 A 1 ATOM 63 N N . GLY A 1 8 ? 1.622 1.613 2.208 1.00 96.72 8 A 1 ATOM 64 C CA . GLY A 1 8 ? 2.264 0.353 1.859 1.00 96.75 8 A 1 ATOM 65 C C . GLY A 1 8 ? 1.940 -0.089 0.449 1.00 97.25 8 A 1 ATOM 66 O O . GLY A 1 8 ? 2.830 -0.467 -0.309 1.00 96.68 8 A 1 ATOM 67 N N . LEU A 1 9 ? 0.656 -0.056 0.082 1.00 96.97 9 A 1 ATOM 68 C CA . LEU A 1 9 ? 0.228 -0.472 -1.250 1.00 96.95 9 A 1 ATOM 69 C C . LEU A 1 9 ? 0.767 0.473 -2.318 1.00 97.16 9 A 1 ATOM 70 O O . LEU A 1 9 ? 1.075 0.053 -3.435 1.00 96.20 9 A 1 ATOM 71 C CB . LEU A 1 9 ? -1.306 -0.539 -1.317 1.00 96.52 9 A 1 ATOM 72 C CG . LEU A 1 9 ? -2.010 0.808 -1.468 1.00 90.83 9 A 1 ATOM 73 C CD1 . LEU A 1 9 ? -2.174 1.170 -2.937 1.00 87.02 9 A 1 ATOM 74 C CD2 . LEU A 1 9 ? -3.385 0.756 -0.808 1.00 87.52 9 A 1 ATOM 75 N N . VAL A 1 10 ? 0.879 1.756 -1.988 1.00 97.53 10 A 1 ATOM 76 C CA . VAL A 1 10 ? 1.394 2.749 -2.928 1.00 97.16 10 A 1 ATOM 77 C C . VAL A 1 10 ? 2.875 2.512 -3.198 1.00 97.14 10 A 1 ATOM 78 O O . VAL A 1 10 ? 3.347 2.681 -4.323 1.00 96.34 10 A 1 ATOM 79 C CB . VAL A 1 10 ? 1.190 4.179 -2.395 1.00 96.49 10 A 1 ATOM 80 C CG1 . VAL A 1 10 ? 1.857 5.198 -3.311 1.00 93.28 10 A 1 ATOM 81 C CG2 . VAL A 1 10 ? -0.289 4.488 -2.267 1.00 93.81 10 A 1 ATOM 82 N N . SER A 1 11 ? 3.598 2.113 -2.165 1.00 97.39 11 A 1 ATOM 83 C CA . SER A 1 11 ? 5.029 1.852 -2.286 1.00 97.47 11 A 1 ATOM 84 C C . SER A 1 11 ? 5.306 0.701 -3.245 1.00 97.48 11 A 1 ATOM 85 O O . SER A 1 11 ? 6.157 0.807 -4.123 1.00 96.56 11 A 1 ATOM 86 C CB . SER A 1 11 ? 5.629 1.534 -0.922 1.00 96.74 11 A 1 ATOM 87 O OG . SER A 1 11 ? 7.021 1.332 -1.028 1.00 88.35 11 A 1 ATOM 88 N N . ILE A 1 12 ? 4.587 -0.411 -3.075 1.00 96.58 12 A 1 ATOM 89 C CA . ILE A 1 12 ? 4.762 -1.577 -3.938 1.00 96.36 12 A 1 ATOM 90 C C . ILE A 1 12 ? 4.253 -1.310 -5.349 1.00 96.38 12 A 1 ATOM 91 O O . ILE A 1 12 ? 4.720 -1.921 -6.307 1.00 95.51 12 A 1 ATOM 92 C CB . ILE A 1 12 ? 4.039 -2.807 -3.366 1.00 95.66 12 A 1 ATOM 93 C CG1 . ILE A 1 12 ? 2.538 -2.552 -3.275 1.00 91.11 12 A 1 ATOM 94 C CG2 . ILE A 1 12 ? 4.612 -3.152 -2.000 1.00 89.71 12 A 1 ATOM 95 C CD1 . ILE A 1 12 ? 1.749 -3.761 -2.821 1.00 84.30 12 A 1 ATOM 96 N N . SER A 1 13 ? 3.293 -0.413 -5.468 1.00 95.72 13 A 1 ATOM 97 C CA . SER A 1 13 ? 2.721 -0.062 -6.765 1.00 95.74 13 A 1 ATOM 98 C C . SER A 1 13 ? 3.742 0.646 -7.651 1.00 96.01 13 A 1 ATOM 99 O O . SER A 1 13 ? 3.635 0.636 -8.876 1.00 94.77 13 A 1 ATOM 100 C CB . SER A 1 13 ? 1.497 0.832 -6.588 1.00 94.12 13 A 1 ATOM 101 O OG . SER A 1 13 ? 0.904 1.118 -7.838 1.00 83.43 13 A 1 ATOM 102 N N . GLU A 1 14 ? 4.734 1.266 -7.028 1.00 93.87 14 A 1 ATOM 103 C CA . GLU A 1 14 ? 5.768 1.995 -7.758 1.00 92.95 14 A 1 ATOM 104 C C . GLU A 1 14 ? 7.036 1.168 -7.924 1.00 92.07 14 A 1 ATOM 105 O O . GLU A 1 14 ? 8.087 1.703 -8.268 1.00 86.58 14 A 1 ATOM 106 C CB . GLU A 1 14 ? 6.102 3.301 -7.029 1.00 90.79 14 A 1 ATOM 107 C CG . GLU A 1 14 ? 4.928 4.262 -6.965 1.00 82.12 14 A 1 ATOM 108 C CD . GLU A 1 14 ? 5.294 5.542 -6.245 1.00 78.59 14 A 1 ATOM 109 O OE1 . GLU A 1 14 ? 6.260 5.524 -5.466 1.00 72.05 14 A 1 ATOM 110 O OE2 . GLU A 1 14 ? 4.617 6.564 -6.459 1.00 73.90 14 A 1 ATOM 111 N N . CYS A 1 15 ? 6.931 -0.147 -7.711 1.00 93.11 15 A 1 ATOM 112 C CA . CYS A 1 15 ? 8.089 -1.033 -7.817 1.00 91.46 15 A 1 ATOM 113 C C . CYS A 1 15 ? 8.620 -1.074 -9.259 1.00 90.22 15 A 1 ATOM 114 O O . CYS A 1 15 ? 9.702 -0.521 -9.507 1.00 86.48 15 A 1 ATOM 115 C CB . CYS A 1 15 ? 7.721 -2.442 -7.343 1.00 86.64 15 A 1 ATOM 116 S SG . CYS A 1 15 ? 7.498 -2.561 -5.570 1.00 79.68 15 A 1 ATOM 117 O OXT . CYS A 1 15 ? 7.950 -1.644 -10.146 1.00 75.90 15 A 1 #