# 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_spkb23694 # _entry.id spkb23694 # 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" "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" "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" "C9 H11 N O3" 181.189 TYR y TYROSINE c1cc(ccc1C[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 LYS 2 1 n GLY 3 1 n TYR 4 1 n LEU 5 1 n SER 6 1 n LEU 7 1 n SER 8 1 n ILE 9 1 n LEU 10 1 n PRO 11 1 n LEU 12 1 n LEU 13 1 n VAL 14 1 n ALA 15 1 n ALA 16 # _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 @ 2025-07-04 04:35:40)" _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 87.23 _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 72.67 1 1 A LYS 2 2 74.84 1 2 A GLY 3 2 84.22 1 3 A TYR 4 2 84.24 1 4 A LEU 5 2 83.66 1 5 A SER 6 2 88.81 1 6 A LEU 7 2 86.79 1 7 A SER 8 2 91.27 1 8 A ILE 9 2 90.57 1 9 A LEU 10 2 91.40 1 10 A PRO 11 2 93.75 1 11 A LEU 12 2 90.95 1 12 A LEU 13 2 92.37 1 13 A VAL 14 2 93.53 1 14 A ALA 15 2 94.56 1 15 A ALA 16 2 90.03 1 16 # _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 GLY . 3 A 3 A 4 1 n TYR . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n SER . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n SER . 8 A 8 A 9 1 n ILE . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n PRO . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n ALA . 16 A 16 # _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 ? -13.114 0.379 0.467 1.00 75.85 1 A 1 ATOM 2 C CA . MET A 1 1 ? -11.987 0.992 -0.251 1.00 78.06 1 A 1 ATOM 3 C C . MET A 1 1 ? -11.233 -0.071 -1.047 1.00 79.61 1 A 1 ATOM 4 O O . MET A 1 1 ? -10.763 -1.058 -0.480 1.00 76.01 1 A 1 ATOM 5 C CB . MET A 1 1 ? -11.014 1.670 0.720 1.00 72.57 1 A 1 ATOM 6 C CG . MET A 1 1 ? -11.632 2.822 1.492 1.00 72.22 1 A 1 ATOM 7 S SD . MET A 1 1 ? -10.483 3.565 2.679 1.00 67.58 1 A 1 ATOM 8 C CE . MET A 1 1 ? -11.515 4.865 3.344 1.00 59.47 1 A 1 ATOM 9 N N . LYS A 1 2 ? -11.139 0.122 -2.345 1.00 80.73 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -10.437 -0.816 -3.216 1.00 83.59 2 A 1 ATOM 11 C C . LYS A 1 2 ? -8.937 -0.503 -3.226 1.00 84.69 2 A 1 ATOM 12 O O . LYS A 1 2 ? -8.544 0.662 -3.276 1.00 80.93 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -11.022 -0.748 -4.628 1.00 79.06 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -12.493 -1.155 -4.695 1.00 73.02 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -13.075 -0.994 -6.093 1.00 70.89 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -12.521 -2.034 -7.054 1.00 64.07 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -13.164 -1.933 -8.392 1.00 56.60 2 A 1 ATOM 18 N N . GLY A 1 3 ? -8.102 -1.547 -3.173 1.00 81.14 3 A 1 ATOM 19 C CA . GLY A 1 3 ? -6.652 -1.358 -3.136 1.00 83.22 3 A 1 ATOM 20 C C . GLY A 1 3 ? -6.155 -0.959 -1.758 1.00 86.98 3 A 1 ATOM 21 O O . GLY A 1 3 ? -5.224 -0.168 -1.634 1.00 85.55 3 A 1 ATOM 22 N N . TYR A 1 4 ? -6.797 -1.500 -0.717 1.00 84.94 4 A 1 ATOM 23 C CA . TYR A 1 4 ? -6.471 -1.173 0.673 1.00 86.99 4 A 1 ATOM 24 C C . TYR A 1 4 ? -5.055 -1.606 1.037 1.00 89.60 4 A 1 ATOM 25 O O . TYR A 1 4 ? -4.246 -0.793 1.491 1.00 87.90 4 A 1 ATOM 26 C CB . TYR A 1 4 ? -7.496 -1.832 1.613 1.00 85.15 4 A 1 ATOM 27 C CG . TYR A 1 4 ? -7.351 -1.418 3.061 1.00 84.01 4 A 1 ATOM 28 C CD1 . TYR A 1 4 ? -6.541 -2.141 3.935 1.00 83.16 4 A 1 ATOM 29 C CD2 . TYR A 1 4 ? -8.023 -0.307 3.553 1.00 82.36 4 A 1 ATOM 30 C CE1 . TYR A 1 4 ? -6.402 -1.760 5.260 1.00 80.82 4 A 1 ATOM 31 C CE2 . TYR A 1 4 ? -7.888 0.083 4.883 1.00 82.09 4 A 1 ATOM 32 C CZ . TYR A 1 4 ? -7.078 -0.652 5.729 1.00 82.80 4 A 1 ATOM 33 O OH . TYR A 1 4 ? -6.945 -0.268 7.046 1.00 81.04 4 A 1 ATOM 34 N N . LEU A 1 5 ? -4.742 -2.880 0.829 1.00 84.88 5 A 1 ATOM 35 C CA . LEU A 1 5 ? -3.430 -3.424 1.171 1.00 86.07 5 A 1 ATOM 36 C C . LEU A 1 5 ? -2.330 -2.882 0.265 1.00 89.01 5 A 1 ATOM 37 O O . LEU A 1 5 ? -1.247 -2.544 0.735 1.00 88.23 5 A 1 ATOM 38 C CB . LEU A 1 5 ? -3.461 -4.953 1.102 1.00 84.36 5 A 1 ATOM 39 C CG . LEU A 1 5 ? -4.324 -5.626 2.169 1.00 81.81 5 A 1 ATOM 40 C CD1 . LEU A 1 5 ? -4.469 -7.107 1.862 1.00 78.82 5 A 1 ATOM 41 C CD2 . LEU A 1 5 ? -3.724 -5.435 3.554 1.00 76.11 5 A 1 ATOM 42 N N . SER A 1 6 ? -2.609 -2.793 -1.018 1.00 89.19 6 A 1 ATOM 43 C CA . SER A 1 6 ? -1.631 -2.328 -2.003 1.00 90.21 6 A 1 ATOM 44 C C . SER A 1 6 ? -1.234 -0.866 -1.791 1.00 92.18 6 A 1 ATOM 45 O O . SER A 1 6 ? -0.090 -0.487 -2.031 1.00 91.23 6 A 1 ATOM 46 C CB . SER A 1 6 ? -2.187 -2.507 -3.412 1.00 88.40 6 A 1 ATOM 47 O OG . SER A 1 6 ? -1.240 -2.119 -4.373 1.00 81.62 6 A 1 ATOM 48 N N . LEU A 1 7 ? -2.170 -0.036 -1.325 1.00 89.52 7 A 1 ATOM 49 C CA . LEU A 1 7 ? -1.932 1.392 -1.144 1.00 90.00 7 A 1 ATOM 50 C C . LEU A 1 7 ? -1.619 1.768 0.305 1.00 92.31 7 A 1 ATOM 51 O O . LEU A 1 7 ? -1.289 2.921 0.588 1.00 90.79 7 A 1 ATOM 52 C CB . LEU A 1 7 ? -3.151 2.182 -1.641 1.00 88.42 7 A 1 ATOM 53 C CG . LEU A 1 7 ? -3.390 2.115 -3.150 1.00 83.77 7 A 1 ATOM 54 C CD1 . LEU A 1 7 ? -4.749 2.719 -3.494 1.00 80.41 7 A 1 ATOM 55 C CD2 . LEU A 1 7 ? -2.291 2.849 -3.901 1.00 79.13 7 A 1 ATOM 56 N N . SER A 1 8 ? -1.712 0.808 1.223 1.00 92.02 8 A 1 ATOM 57 C CA . SER A 1 8 ? -1.493 1.077 2.643 1.00 92.61 8 A 1 ATOM 58 C C . SER A 1 8 ? -0.283 0.337 3.213 1.00 94.13 8 A 1 ATOM 59 O O . SER A 1 8 ? 0.430 0.873 4.058 1.00 93.03 8 A 1 ATOM 60 C CB . SER A 1 8 ? -2.741 0.720 3.451 1.00 90.85 8 A 1 ATOM 61 O OG . SER A 1 8 ? -3.844 1.510 3.036 1.00 85.01 8 A 1 ATOM 62 N N . ILE A 1 9 ? -0.042 -0.890 2.749 1.00 92.32 9 A 1 ATOM 63 C CA . ILE A 1 9 ? 1.051 -1.701 3.265 1.00 92.66 9 A 1 ATOM 64 C C . ILE A 1 9 ? 2.413 -1.264 2.722 1.00 94.08 9 A 1 ATOM 65 O O . ILE A 1 9 ? 3.411 -1.295 3.446 1.00 92.94 9 A 1 ATOM 66 C CB . ILE A 1 9 ? 0.799 -3.205 2.982 1.00 92.07 9 A 1 ATOM 67 C CG1 . ILE A 1 9 ? 1.628 -4.092 3.917 1.00 89.27 9 A 1 ATOM 68 C CG2 . ILE A 1 9 ? 1.088 -3.555 1.527 1.00 87.63 9 A 1 ATOM 69 C CD1 . ILE A 1 9 ? 1.179 -4.035 5.368 1.00 83.63 9 A 1 ATOM 70 N N . LEU A 1 10 ? 2.461 -0.843 1.464 1.00 93.89 10 A 1 ATOM 71 C CA . LEU A 1 10 ? 3.714 -0.430 0.833 1.00 93.84 10 A 1 ATOM 72 C C . LEU A 1 10 ? 4.281 0.862 1.436 1.00 95.11 10 A 1 ATOM 73 O O . LEU A 1 10 ? 5.448 0.885 1.834 1.00 95.03 10 A 1 ATOM 74 C CB . LEU A 1 10 ? 3.539 -0.312 -0.692 1.00 92.97 10 A 1 ATOM 75 C CG . LEU A 1 10 ? 4.236 -1.414 -1.499 1.00 88.59 10 A 1 ATOM 76 C CD1 . LEU A 1 10 ? 5.740 -1.318 -1.377 1.00 86.06 10 A 1 ATOM 77 C CD2 . LEU A 1 10 ? 3.734 -2.786 -1.069 1.00 85.71 10 A 1 ATOM 78 N N . PRO A 1 11 ? 3.499 1.948 1.524 1.00 94.62 11 A 1 ATOM 79 C CA . PRO A 1 11 ? 3.993 3.179 2.163 1.00 94.46 11 A 1 ATOM 80 C C . PRO A 1 11 ? 4.331 2.973 3.636 1.00 95.38 11 A 1 ATOM 81 O O . PRO A 1 11 ? 5.226 3.636 4.161 1.00 94.15 11 A 1 ATOM 82 C CB . PRO A 1 11 ? 2.837 4.177 1.997 1.00 92.69 11 A 1 ATOM 83 C CG . PRO A 1 11 ? 1.637 3.350 1.701 1.00 91.43 11 A 1 ATOM 84 C CD . PRO A 1 11 ? 2.160 2.151 0.965 1.00 93.50 11 A 1 ATOM 85 N N . LEU A 1 12 ? 3.653 2.053 4.294 1.00 92.90 12 A 1 ATOM 86 C CA . LEU A 1 12 ? 3.941 1.715 5.684 1.00 93.25 12 A 1 ATOM 87 C C . LEU A 1 12 ? 5.317 1.061 5.808 1.00 94.78 12 A 1 ATOM 88 O O . LEU A 1 12 ? 6.073 1.365 6.733 1.00 93.59 12 A 1 ATOM 89 C CB . LEU A 1 12 ? 2.857 0.775 6.229 1.00 92.26 12 A 1 ATOM 90 C CG . LEU A 1 12 ? 2.957 0.460 7.726 1.00 88.91 12 A 1 ATOM 91 C CD1 . LEU A 1 12 ? 2.630 1.688 8.569 1.00 86.31 12 A 1 ATOM 92 C CD2 . LEU A 1 12 ? 2.013 -0.683 8.085 1.00 85.64 12 A 1 ATOM 93 N N . LEU A 1 13 ? 5.642 0.169 4.872 1.00 93.71 13 A 1 ATOM 94 C CA . LEU A 1 13 ? 6.926 -0.527 4.851 1.00 94.03 13 A 1 ATOM 95 C C . LEU A 1 13 ? 8.071 0.434 4.527 1.00 95.56 13 A 1 ATOM 96 O O . LEU A 1 13 ? 9.159 0.336 5.092 1.00 95.29 13 A 1 ATOM 97 C CB . LEU A 1 13 ? 6.878 -1.679 3.829 1.00 93.40 13 A 1 ATOM 98 C CG . LEU A 1 13 ? 7.428 -3.023 4.321 1.00 90.67 13 A 1 ATOM 99 C CD1 . LEU A 1 13 ? 8.875 -2.935 4.757 1.00 88.18 13 A 1 ATOM 100 C CD2 . LEU A 1 13 ? 6.554 -3.574 5.443 1.00 88.09 13 A 1 ATOM 101 N N . VAL A 1 14 ? 7.828 1.363 3.621 1.00 94.72 14 A 1 ATOM 102 C CA . VAL A 1 14 ? 8.817 2.378 3.241 1.00 94.63 14 A 1 ATOM 103 C C . VAL A 1 14 ? 9.102 3.328 4.405 1.00 95.73 14 A 1 ATOM 104 O O . VAL A 1 14 ? 10.231 3.796 4.584 1.00 95.50 14 A 1 ATOM 105 C CB . VAL A 1 14 ? 8.339 3.171 2.004 1.00 93.35 14 A 1 ATOM 106 C CG1 . VAL A 1 14 ? 9.306 4.306 1.663 1.00 90.28 14 A 1 ATOM 107 C CG2 . VAL A 1 14 ? 8.200 2.248 0.801 1.00 90.48 14 A 1 ATOM 108 N N . ALA A 1 15 ? 8.098 3.613 5.205 1.00 95.08 15 A 1 ATOM 109 C CA . ALA A 1 15 ? 8.221 4.492 6.367 1.00 94.63 15 A 1 ATOM 110 C C . ALA A 1 15 ? 8.730 3.758 7.615 1.00 95.28 15 A 1 ATOM 111 O O . ALA A 1 15 ? 8.852 4.360 8.683 1.00 94.36 15 A 1 ATOM 112 C CB . ALA A 1 15 ? 6.871 5.159 6.653 1.00 93.45 15 A 1 ATOM 113 N N . ALA A 1 16 ? 9.027 2.475 7.479 1.00 94.28 16 A 1 ATOM 114 C CA . ALA A 1 16 ? 9.506 1.657 8.582 1.00 92.85 16 A 1 ATOM 115 C C . ALA A 1 16 ? 11.018 1.413 8.474 1.00 91.47 16 A 1 ATOM 116 O O . ALA A 1 16 ? 11.627 1.773 7.448 1.00 89.40 16 A 1 ATOM 117 C CB . ALA A 1 16 ? 8.736 0.337 8.621 1.00 89.84 16 A 1 ATOM 118 O OXT . ALA A 1 16 ? 11.607 0.855 9.411 1.00 82.35 16 A 1 #