# 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_spkb28825 # _entry.id spkb28825 # 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" "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" "C4 H9 N O3" 119.119 THR y THREONINE C[C@H]([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 THR 2 1 n LYS 3 1 n TRP 4 1 n LEU 5 1 n LEU 6 1 n LEU 7 1 n MET 8 1 n VAL 9 1 n CYS 10 1 n LEU 11 1 n GLY 12 1 n ILE 13 1 n ALA 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 @ 2025-07-03 23:46:02)" _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 93.21 _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 81.26 1 1 A THR 2 2 89.13 1 2 A LYS 3 2 90.53 1 3 A TRP 4 2 93.24 1 4 A LEU 5 2 94.64 1 5 A LEU 6 2 94.40 1 6 A LEU 7 2 94.79 1 7 A MET 8 2 93.93 1 8 A VAL 9 2 97.33 1 9 A CYS 10 2 97.27 1 10 A LEU 11 2 96.55 1 11 A GLY 12 2 97.45 1 12 A ILE 13 2 94.70 1 13 A ALA 14 2 96.45 1 14 A CYS 15 2 90.91 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 THR . 2 A 2 A 3 1 n LYS . 3 A 3 A 4 1 n TRP . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n MET . 8 A 8 A 9 1 n VAL . 9 A 9 A 10 1 n CYS . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n GLY . 12 A 12 A 13 1 n ILE . 13 A 13 A 14 1 n ALA . 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 ? 4.319 9.647 -3.216 1.00 87.59 1 A 1 ATOM 2 C CA . MET A 1 1 ? 4.909 8.534 -2.451 1.00 87.87 1 A 1 ATOM 3 C C . MET A 1 1 ? 3.833 7.810 -1.644 1.00 89.29 1 A 1 ATOM 4 O O . MET A 1 1 ? 4.126 6.889 -0.890 1.00 86.50 1 A 1 ATOM 5 C CB . MET A 1 1 ? 5.976 9.071 -1.494 1.00 82.77 1 A 1 ATOM 6 C CG . MET A 1 1 ? 7.077 9.813 -2.229 1.00 77.55 1 A 1 ATOM 7 S SD . MET A 1 1 ? 8.294 10.492 -1.107 1.00 74.13 1 A 1 ATOM 8 C CE . MET A 1 1 ? 9.276 11.429 -2.254 1.00 64.35 1 A 1 ATOM 9 N N . THR A 1 2 ? 2.612 8.240 -1.819 1.00 90.55 2 A 1 ATOM 10 C CA . THR A 1 2 ? 1.485 7.645 -1.100 1.00 92.60 2 A 1 ATOM 11 C C . THR A 1 2 ? 1.084 6.302 -1.702 1.00 93.89 2 A 1 ATOM 12 O O . THR A 1 2 ? 0.235 5.596 -1.167 1.00 91.18 2 A 1 ATOM 13 C CB . THR A 1 2 ? 0.287 8.594 -1.130 1.00 90.28 2 A 1 ATOM 14 O OG1 . THR A 1 2 ? 0.708 9.914 -0.793 1.00 83.78 2 A 1 ATOM 15 C CG2 . THR A 1 2 ? -0.779 8.162 -0.140 1.00 81.65 2 A 1 ATOM 16 N N . LYS A 1 3 ? 1.712 5.952 -2.822 1.00 95.87 3 A 1 ATOM 17 C CA . LYS A 1 3 ? 1.400 4.684 -3.483 1.00 95.98 3 A 1 ATOM 18 C C . LYS A 1 3 ? 1.754 3.505 -2.583 1.00 96.82 3 A 1 ATOM 19 O O . LYS A 1 3 ? 1.211 2.415 -2.728 1.00 96.43 3 A 1 ATOM 20 C CB . LYS A 1 3 ? 2.159 4.571 -4.804 1.00 94.80 3 A 1 ATOM 21 C CG . LYS A 1 3 ? 1.743 3.338 -5.584 1.00 90.78 3 A 1 ATOM 22 C CD . LYS A 1 3 ? 2.549 3.185 -6.857 1.00 87.57 3 A 1 ATOM 23 C CE . LYS A 1 3 ? 2.131 1.923 -7.605 1.00 81.43 3 A 1 ATOM 24 N NZ . LYS A 1 3 ? 2.972 1.697 -8.802 1.00 75.10 3 A 1 ATOM 25 N N . TRP A 1 4 ? 2.672 3.735 -1.651 1.00 95.15 4 A 1 ATOM 26 C CA . TRP A 1 4 ? 3.084 2.687 -0.720 1.00 95.60 4 A 1 ATOM 27 C C . TRP A 1 4 ? 1.892 2.204 0.085 1.00 96.07 4 A 1 ATOM 28 O O . TRP A 1 4 ? 1.830 1.044 0.485 1.00 95.21 4 A 1 ATOM 29 C CB . TRP A 1 4 ? 4.182 3.226 0.205 1.00 95.51 4 A 1 ATOM 30 C CG . TRP A 1 4 ? 5.545 2.678 -0.118 1.00 94.85 4 A 1 ATOM 31 C CD1 . TRP A 1 4 ? 6.569 2.509 0.770 1.00 91.85 4 A 1 ATOM 32 C CD2 . TRP A 1 4 ? 6.054 2.219 -1.383 1.00 94.04 4 A 1 ATOM 33 N NE1 . TRP A 1 4 ? 7.665 1.986 0.130 1.00 91.40 4 A 1 ATOM 34 C CE2 . TRP A 1 4 ? 7.379 1.790 -1.198 1.00 93.66 4 A 1 ATOM 35 C CE3 . TRP A 1 4 ? 5.515 2.120 -2.671 1.00 91.85 4 A 1 ATOM 36 C CZ2 . TRP A 1 4 ? 8.159 1.285 -2.244 1.00 92.26 4 A 1 ATOM 37 C CZ3 . TRP A 1 4 ? 6.296 1.615 -3.710 1.00 88.84 4 A 1 ATOM 38 C CH2 . TRP A 1 4 ? 7.600 1.206 -3.494 1.00 89.06 4 A 1 ATOM 39 N N . LEU A 1 5 ? 0.943 3.089 0.319 1.00 96.89 5 A 1 ATOM 40 C CA . LEU A 1 5 ? -0.260 2.725 1.056 1.00 96.81 5 A 1 ATOM 41 C C . LEU A 1 5 ? -1.063 1.687 0.285 1.00 97.22 5 A 1 ATOM 42 O O . LEU A 1 5 ? -1.694 0.817 0.882 1.00 97.13 5 A 1 ATOM 43 C CB . LEU A 1 5 ? -1.114 3.965 1.306 1.00 96.78 5 A 1 ATOM 44 C CG . LEU A 1 5 ? -0.485 4.953 2.287 1.00 93.28 5 A 1 ATOM 45 C CD1 . LEU A 1 5 ? -1.321 6.224 2.359 1.00 89.04 5 A 1 ATOM 46 C CD2 . LEU A 1 5 ? -0.370 4.335 3.671 1.00 89.95 5 A 1 ATOM 47 N N . LEU A 1 6 ? -1.028 1.777 -1.037 1.00 96.99 6 A 1 ATOM 48 C CA . LEU A 1 6 ? -1.746 0.822 -1.877 1.00 96.73 6 A 1 ATOM 49 C C . LEU A 1 6 ? -1.177 -0.579 -1.691 1.00 97.02 6 A 1 ATOM 50 O O . LEU A 1 6 ? -1.919 -1.559 -1.651 1.00 96.85 6 A 1 ATOM 51 C CB . LEU A 1 6 ? -1.639 1.237 -3.345 1.00 96.57 6 A 1 ATOM 52 C CG . LEU A 1 6 ? -2.404 2.514 -3.671 1.00 92.23 6 A 1 ATOM 53 C CD1 . LEU A 1 6 ? -2.087 2.960 -5.091 1.00 89.07 6 A 1 ATOM 54 C CD2 . LEU A 1 6 ? -3.903 2.287 -3.530 1.00 89.71 6 A 1 ATOM 55 N N . LEU A 1 7 ? 0.136 -0.658 -1.568 1.00 97.22 7 A 1 ATOM 56 C CA . LEU A 1 7 ? 0.790 -1.943 -1.357 1.00 97.07 7 A 1 ATOM 57 C C . LEU A 1 7 ? 0.495 -2.464 0.043 1.00 97.43 7 A 1 ATOM 58 O O . LEU A 1 7 ? 0.260 -3.655 0.235 1.00 97.37 7 A 1 ATOM 59 C CB . LEU A 1 7 ? 2.298 -1.793 -1.553 1.00 96.94 7 A 1 ATOM 60 C CG . LEU A 1 7 ? 2.695 -1.476 -2.992 1.00 93.07 7 A 1 ATOM 61 C CD1 . LEU A 1 7 ? 4.187 -1.184 -3.068 1.00 89.09 7 A 1 ATOM 62 C CD2 . LEU A 1 7 ? 2.346 -2.638 -3.913 1.00 90.14 7 A 1 ATOM 63 N N . MET A 1 8 ? 0.508 -1.556 1.008 1.00 97.17 8 A 1 ATOM 64 C CA . MET A 1 8 ? 0.212 -1.930 2.388 1.00 96.81 8 A 1 ATOM 65 C C . MET A 1 8 ? -1.219 -2.433 2.511 1.00 97.26 8 A 1 ATOM 66 O O . MET A 1 8 ? -1.490 -3.373 3.257 1.00 96.83 8 A 1 ATOM 67 C CB . MET A 1 8 ? 0.428 -0.728 3.306 1.00 96.38 8 A 1 ATOM 68 C CG . MET A 1 8 ? 1.908 -0.380 3.435 1.00 94.26 8 A 1 ATOM 69 S SD . MET A 1 8 ? 2.809 -1.618 4.356 1.00 90.12 8 A 1 ATOM 70 C CE . MET A 1 8 ? 4.459 -0.933 4.277 1.00 82.60 8 A 1 ATOM 71 N N . VAL A 1 9 ? -2.109 -1.819 1.763 1.00 97.90 9 A 1 ATOM 72 C CA . VAL A 1 9 ? -3.514 -2.225 1.782 1.00 97.77 9 A 1 ATOM 73 C C . VAL A 1 9 ? -3.646 -3.669 1.303 1.00 97.93 9 A 1 ATOM 74 O O . VAL A 1 9 ? -4.411 -4.451 1.869 1.00 97.65 9 A 1 ATOM 75 C CB . VAL A 1 9 ? -4.359 -1.292 0.904 1.00 97.49 9 A 1 ATOM 76 C CG1 . VAL A 1 9 ? -5.766 -1.840 0.723 1.00 96.29 9 A 1 ATOM 77 C CG2 . VAL A 1 9 ? -4.436 0.087 1.537 1.00 96.27 9 A 1 ATOM 78 N N . CYS A 1 10 ? -2.892 -4.014 0.285 1.00 97.85 10 A 1 ATOM 79 C CA . CYS A 1 10 ? -2.917 -5.374 -0.242 1.00 97.77 10 A 1 ATOM 80 C C . CYS A 1 10 ? -2.441 -6.377 0.798 1.00 97.85 10 A 1 ATOM 81 O O . CYS A 1 10 ? -2.999 -7.457 0.929 1.00 96.94 10 A 1 ATOM 82 C CB . CYS A 1 10 ? -2.042 -5.464 -1.486 1.00 97.27 10 A 1 ATOM 83 S SG . CYS A 1 10 ? -2.899 -4.962 -2.984 1.00 95.94 10 A 1 ATOM 84 N N . LEU A 1 11 ? -1.411 -5.995 1.542 1.00 97.77 11 A 1 ATOM 85 C CA . LEU A 1 11 ? -0.869 -6.870 2.574 1.00 97.70 11 A 1 ATOM 86 C C . LEU A 1 11 ? -1.886 -7.091 3.681 1.00 97.92 11 A 1 ATOM 87 O O . LEU A 1 11 ? -1.987 -8.190 4.226 1.00 97.27 11 A 1 ATOM 88 C CB . LEU A 1 11 ? 0.406 -6.253 3.152 1.00 97.39 11 A 1 ATOM 89 C CG . LEU A 1 11 ? 1.557 -6.199 2.150 1.00 96.29 11 A 1 ATOM 90 C CD1 . LEU A 1 11 ? 2.717 -5.409 2.734 1.00 94.20 11 A 1 ATOM 91 C CD2 . LEU A 1 11 ? 2.009 -7.604 1.788 1.00 93.85 11 A 1 ATOM 92 N N . GLY A 1 12 ? -2.625 -6.043 4.007 1.00 97.54 12 A 1 ATOM 93 C CA . GLY A 1 12 ? -3.640 -6.134 5.050 1.00 97.45 12 A 1 ATOM 94 C C . GLY A 1 12 ? -4.888 -6.850 4.579 1.00 97.73 12 A 1 ATOM 95 O O . GLY A 1 12 ? -5.453 -7.672 5.302 1.00 97.07 12 A 1 ATOM 96 N N . ILE A 1 13 ? -5.317 -6.533 3.357 1.00 96.99 13 A 1 ATOM 97 C CA . ILE A 1 13 ? -6.515 -7.143 2.781 1.00 96.77 13 A 1 ATOM 98 C C . ILE A 1 13 ? -6.165 -8.415 2.020 1.00 96.95 13 A 1 ATOM 99 O O . ILE A 1 13 ? -7.033 -9.227 1.711 1.00 95.85 13 A 1 ATOM 100 C CB . ILE A 1 13 ? -7.225 -6.143 1.856 1.00 95.93 13 A 1 ATOM 101 C CG1 . ILE A 1 13 ? -7.586 -4.876 2.645 1.00 93.37 13 A 1 ATOM 102 C CG2 . ILE A 1 13 ? -8.486 -6.759 1.262 1.00 92.77 13 A 1 ATOM 103 C CD1 . ILE A 1 13 ? -8.146 -3.772 1.770 1.00 89.00 13 A 1 ATOM 104 N N . ALA A 1 14 ? -4.883 -8.599 1.756 1.00 96.93 14 A 1 ATOM 105 C CA . ALA A 1 14 ? -4.391 -9.750 0.994 1.00 96.85 14 A 1 ATOM 106 C C . ALA A 1 14 ? -5.040 -9.799 -0.387 1.00 97.05 14 A 1 ATOM 107 O O . ALA A 1 14 ? -5.731 -10.760 -0.729 1.00 95.55 14 A 1 ATOM 108 C CB . ALA A 1 14 ? -4.658 -11.038 1.768 1.00 95.89 14 A 1 ATOM 109 N N . CYS A 1 15 ? -4.821 -8.728 -1.155 1.00 95.01 15 A 1 ATOM 110 C CA . CYS A 1 15 ? -5.408 -8.635 -2.491 1.00 94.31 15 A 1 ATOM 111 C C . CYS A 1 15 ? -4.785 -9.671 -3.434 1.00 93.18 15 A 1 ATOM 112 O O . CYS A 1 15 ? -3.761 -10.275 -3.082 1.00 88.94 15 A 1 ATOM 113 C CB . CYS A 1 15 ? -5.209 -7.227 -3.051 1.00 91.16 15 A 1 ATOM 114 S SG . CYS A 1 15 ? -3.524 -6.871 -3.591 1.00 87.61 15 A 1 ATOM 115 O OXT . CYS A 1 15 ? -5.324 -9.871 -4.539 1.00 86.19 15 A 1 #