# 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_spkb23802 # _entry.id spkb23802 # 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 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" # _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 LYS 3 1 n TYR 4 1 n LEU 5 1 n ALA 6 1 n LEU 7 1 n ALA 8 1 n LEU 9 1 n ILE 10 1 n ALA 11 1 n PRO 12 1 n LEU 13 1 n LEU 14 1 n ILE 15 1 n SER 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 @ 2025-07-06 10:25:11)" _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 93.46 _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 91.38 1 1 A LYS 2 2 90.77 1 2 A LYS 3 2 90.91 1 3 A TYR 4 2 94.61 1 4 A LEU 5 2 93.62 1 5 A ALA 6 2 97.08 1 6 A LEU 7 2 95.02 1 7 A ALA 8 2 97.56 1 8 A LEU 9 2 95.61 1 9 A ILE 10 2 95.25 1 10 A ALA 11 2 96.96 1 11 A PRO 12 2 96.67 1 12 A LEU 13 2 92.84 1 13 A LEU 14 2 92.23 1 14 A ILE 15 2 93.24 1 15 A SER 16 2 85.29 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 LYS . 3 A 3 A 4 1 n TYR . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n ALA . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n ILE . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n PRO . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n ILE . 15 A 15 A 16 1 n SER . 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 ? -3.058 -0.994 12.070 1.00 96.19 1 A 1 ATOM 2 C CA . MET A 1 1 ? -4.122 -1.566 11.207 1.00 96.82 1 A 1 ATOM 3 C C . MET A 1 1 ? -3.549 -1.924 9.838 1.00 96.97 1 A 1 ATOM 4 O O . MET A 1 1 ? -2.673 -1.238 9.325 1.00 96.33 1 A 1 ATOM 5 C CB . MET A 1 1 ? -5.254 -0.569 11.035 1.00 94.51 1 A 1 ATOM 6 C CG . MET A 1 1 ? -6.043 -0.345 12.328 1.00 88.07 1 A 1 ATOM 7 S SD . MET A 1 1 ? -4.995 0.040 13.740 1.00 84.78 1 A 1 ATOM 8 C CE . MET A 1 1 ? -6.227 0.290 14.991 1.00 77.40 1 A 1 ATOM 9 N N . LYS A 1 2 ? -4.055 -2.997 9.243 1.00 96.73 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -3.563 -3.483 7.954 1.00 97.40 2 A 1 ATOM 11 C C . LYS A 1 2 ? -3.792 -2.478 6.827 1.00 97.66 2 A 1 ATOM 12 O O . LYS A 1 2 ? -2.985 -2.394 5.897 1.00 96.91 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -4.252 -4.802 7.599 1.00 96.46 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -3.915 -5.930 8.567 1.00 90.12 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -2.436 -6.252 8.539 1.00 87.64 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -2.094 -7.383 9.490 1.00 80.62 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -2.776 -8.642 9.101 1.00 73.42 2 A 1 ATOM 18 N N . LYS A 1 3 ? -4.874 -1.707 6.896 1.00 97.41 3 A 1 ATOM 19 C CA . LYS A 1 3 ? -5.169 -0.720 5.860 1.00 97.52 3 A 1 ATOM 20 C C . LYS A 1 3 ? -4.076 0.335 5.779 1.00 97.66 3 A 1 ATOM 21 O O . LYS A 1 3 ? -3.740 0.809 4.695 1.00 96.99 3 A 1 ATOM 22 C CB . LYS A 1 3 ? -6.516 -0.064 6.127 1.00 96.79 3 A 1 ATOM 23 C CG . LYS A 1 3 ? -7.686 -1.027 5.992 1.00 90.98 3 A 1 ATOM 24 C CD . LYS A 1 3 ? -7.781 -1.575 4.587 1.00 87.02 3 A 1 ATOM 25 C CE . LYS A 1 3 ? -8.955 -2.522 4.420 1.00 80.70 3 A 1 ATOM 26 N NZ . LYS A 1 3 ? -9.008 -3.095 3.054 1.00 73.10 3 A 1 ATOM 27 N N . TYR A 1 4 ? -3.512 0.704 6.904 1.00 97.32 4 A 1 ATOM 28 C CA . TYR A 1 4 ? -2.445 1.694 6.923 1.00 97.29 4 A 1 ATOM 29 C C . TYR A 1 4 ? -1.198 1.146 6.239 1.00 97.23 4 A 1 ATOM 30 O O . TYR A 1 4 ? -0.417 1.901 5.656 1.00 96.44 4 A 1 ATOM 31 C CB . TYR A 1 4 ? -2.114 2.094 8.360 1.00 97.08 4 A 1 ATOM 32 C CG . TYR A 1 4 ? -3.231 2.884 9.001 1.00 95.46 4 A 1 ATOM 33 C CD1 . TYR A 1 4 ? -3.422 4.220 8.680 1.00 92.34 4 A 1 ATOM 34 C CD2 . TYR A 1 4 ? -4.088 2.284 9.906 1.00 93.41 4 A 1 ATOM 35 C CE1 . TYR A 1 4 ? -4.454 4.948 9.255 1.00 92.17 4 A 1 ATOM 36 C CE2 . TYR A 1 4 ? -5.127 3.003 10.486 1.00 92.76 4 A 1 ATOM 37 C CZ . TYR A 1 4 ? -5.300 4.334 10.157 1.00 92.99 4 A 1 ATOM 38 O OH . TYR A 1 4 ? -6.324 5.041 10.729 1.00 90.89 4 A 1 ATOM 39 N N . LEU A 1 5 ? -1.020 -0.162 6.284 1.00 97.27 5 A 1 ATOM 40 C CA . LEU A 1 5 ? 0.117 -0.793 5.633 1.00 96.98 5 A 1 ATOM 41 C C . LEU A 1 5 ? -0.011 -0.661 4.121 1.00 97.10 5 A 1 ATOM 42 O O . LEU A 1 5 ? 0.973 -0.403 3.427 1.00 96.71 5 A 1 ATOM 43 C CB . LEU A 1 5 ? 0.190 -2.269 6.018 1.00 96.74 5 A 1 ATOM 44 C CG . LEU A 1 5 ? 0.497 -2.515 7.491 1.00 90.42 5 A 1 ATOM 45 C CD1 . LEU A 1 5 ? 0.435 -4.003 7.790 1.00 86.32 5 A 1 ATOM 46 C CD2 . LEU A 1 5 ? 1.868 -1.968 7.847 1.00 87.40 5 A 1 ATOM 47 N N . ALA A 1 6 ? -1.222 -0.825 3.619 1.00 97.36 6 A 1 ATOM 48 C CA . ALA A 1 6 ? -1.477 -0.695 2.192 1.00 97.12 6 A 1 ATOM 49 C C . ALA A 1 6 ? -1.213 0.733 1.730 1.00 97.45 6 A 1 ATOM 50 O O . ALA A 1 6 ? -0.579 0.957 0.698 1.00 96.85 6 A 1 ATOM 51 C CB . ALA A 1 6 ? -2.916 -1.086 1.886 1.00 96.63 6 A 1 ATOM 52 N N . LEU A 1 7 ? -1.679 1.699 2.508 1.00 97.72 7 A 1 ATOM 53 C CA . LEU A 1 7 ? -1.481 3.107 2.179 1.00 97.63 7 A 1 ATOM 54 C C . LEU A 1 7 ? -0.001 3.454 2.218 1.00 97.86 7 A 1 ATOM 55 O O . LEU A 1 7 ? 0.485 4.237 1.400 1.00 97.52 7 A 1 ATOM 56 C CB . LEU A 1 7 ? -2.244 3.985 3.168 1.00 97.11 7 A 1 ATOM 57 C CG . LEU A 1 7 ? -3.760 3.837 3.098 1.00 92.82 7 A 1 ATOM 58 C CD1 . LEU A 1 7 ? -4.408 4.632 4.217 1.00 89.55 7 A 1 ATOM 59 C CD2 . LEU A 1 7 ? -4.278 4.295 1.747 1.00 89.95 7 A 1 ATOM 60 N N . ALA A 1 8 ? 0.710 2.874 3.155 1.00 97.76 8 A 1 ATOM 61 C CA . ALA A 1 8 ? 2.137 3.116 3.300 1.00 97.63 8 A 1 ATOM 62 C C . ALA A 1 8 ? 2.912 2.567 2.109 1.00 97.85 8 A 1 ATOM 63 O O . ALA A 1 8 ? 4.007 3.039 1.808 1.00 97.22 8 A 1 ATOM 64 C CB . ALA A 1 8 ? 2.643 2.480 4.587 1.00 97.33 8 A 1 ATOM 65 N N . LEU A 1 9 ? 2.354 1.574 1.431 1.00 97.67 9 A 1 ATOM 66 C CA . LEU A 1 9 ? 2.998 0.979 0.268 1.00 97.69 9 A 1 ATOM 67 C C . LEU A 1 9 ? 2.645 1.732 -1.004 1.00 98.05 9 A 1 ATOM 68 O O . LEU A 1 9 ? 3.453 1.810 -1.930 1.00 97.66 9 A 1 ATOM 69 C CB . LEU A 1 9 ? 2.569 -0.480 0.131 1.00 97.31 9 A 1 ATOM 70 C CG . LEU A 1 9 ? 3.061 -1.383 1.256 1.00 94.14 9 A 1 ATOM 71 C CD1 . LEU A 1 9 ? 2.454 -2.770 1.105 1.00 90.84 9 A 1 ATOM 72 C CD2 . LEU A 1 9 ? 4.577 -1.472 1.242 1.00 91.51 9 A 1 ATOM 73 N N . ILE A 1 10 ? 1.446 2.279 -1.058 1.00 96.96 10 A 1 ATOM 74 C CA . ILE A 1 10 ? 0.981 3.008 -2.230 1.00 96.89 10 A 1 ATOM 75 C C . ILE A 1 10 ? 1.747 4.310 -2.431 1.00 97.47 10 A 1 ATOM 76 O O . ILE A 1 10 ? 2.214 4.597 -3.533 1.00 96.88 10 A 1 ATOM 77 C CB . ILE A 1 10 ? -0.522 3.308 -2.122 1.00 96.29 10 A 1 ATOM 78 C CG1 . ILE A 1 10 ? -1.317 2.001 -2.096 1.00 93.68 10 A 1 ATOM 79 C CG2 . ILE A 1 10 ? -0.969 4.173 -3.296 1.00 93.11 10 A 1 ATOM 80 C CD1 . ILE A 1 10 ? -2.778 2.193 -1.749 1.00 90.73 10 A 1 ATOM 81 N N . ALA A 1 11 ? 1.862 5.109 -1.376 1.00 97.25 11 A 1 ATOM 82 C CA . ALA A 1 11 ? 2.539 6.402 -1.468 1.00 97.18 11 A 1 ATOM 83 C C . ALA A 1 11 ? 3.974 6.289 -1.990 1.00 97.57 11 A 1 ATOM 84 O O . ALA A 1 11 ? 4.320 6.925 -2.985 1.00 96.52 11 A 1 ATOM 85 C CB . ALA A 1 11 ? 2.503 7.109 -0.119 1.00 96.26 11 A 1 ATOM 86 N N . PRO A 1 12 ? 4.826 5.506 -1.342 1.00 97.74 12 A 1 ATOM 87 C CA . PRO A 1 12 ? 6.218 5.363 -1.789 1.00 97.26 12 A 1 ATOM 88 C C . PRO A 1 12 ? 6.331 4.679 -3.142 1.00 97.61 12 A 1 ATOM 89 O O . PRO A 1 12 ? 7.252 4.973 -3.904 1.00 96.42 12 A 1 ATOM 90 C CB . PRO A 1 12 ? 6.863 4.519 -0.691 1.00 95.95 12 A 1 ATOM 91 C CG . PRO A 1 12 ? 5.728 3.777 -0.084 1.00 94.79 12 A 1 ATOM 92 C CD . PRO A 1 12 ? 4.570 4.737 -0.136 1.00 96.89 12 A 1 ATOM 93 N N . LEU A 1 13 ? 5.417 3.791 -3.457 1.00 95.80 13 A 1 ATOM 94 C CA . LEU A 1 13 ? 5.427 3.092 -4.735 1.00 96.07 13 A 1 ATOM 95 C C . LEU A 1 13 ? 5.191 4.062 -5.885 1.00 96.66 13 A 1 ATOM 96 O O . LEU A 1 13 ? 5.776 3.909 -6.961 1.00 94.99 13 A 1 ATOM 97 C CB . LEU A 1 13 ? 4.345 2.011 -4.749 1.00 95.49 13 A 1 ATOM 98 C CG . LEU A 1 13 ? 4.313 1.184 -6.029 1.00 90.83 13 A 1 ATOM 99 C CD1 . LEU A 1 13 ? 5.615 0.418 -6.192 1.00 86.22 13 A 1 ATOM 100 C CD2 . LEU A 1 13 ? 3.137 0.224 -5.988 1.00 86.70 13 A 1 ATOM 101 N N . LEU A 1 14 ? 4.347 5.063 -5.672 1.00 95.90 14 A 1 ATOM 102 C CA . LEU A 1 14 ? 4.032 6.046 -6.700 1.00 95.64 14 A 1 ATOM 103 C C . LEU A 1 14 ? 5.120 7.101 -6.827 1.00 95.80 14 A 1 ATOM 104 O O . LEU A 1 14 ? 5.491 7.491 -7.935 1.00 93.99 14 A 1 ATOM 105 C CB . LEU A 1 14 ? 2.698 6.721 -6.379 1.00 94.76 14 A 1 ATOM 106 C CG . LEU A 1 14 ? 1.500 5.777 -6.421 1.00 90.89 14 A 1 ATOM 107 C CD1 . LEU A 1 14 ? 0.255 6.504 -5.943 1.00 85.65 14 A 1 ATOM 108 C CD2 . LEU A 1 14 ? 1.294 5.249 -7.830 1.00 85.23 14 A 1 ATOM 109 N N . ILE A 1 15 ? 5.623 7.586 -5.709 1.00 96.43 15 A 1 ATOM 110 C CA . ILE A 1 15 ? 6.656 8.616 -5.710 1.00 95.83 15 A 1 ATOM 111 C C . ILE A 1 15 ? 8.047 8.038 -5.940 1.00 95.99 15 A 1 ATOM 112 O O . ILE A 1 15 ? 8.964 8.754 -6.347 1.00 94.73 15 A 1 ATOM 113 C CB . ILE A 1 15 ? 6.647 9.394 -4.385 1.00 94.94 15 A 1 ATOM 114 C CG1 . ILE A 1 15 ? 6.931 8.461 -3.209 1.00 91.92 15 A 1 ATOM 115 C CG2 . ILE A 1 15 ? 5.303 10.083 -4.207 1.00 90.49 15 A 1 ATOM 116 C CD1 . ILE A 1 15 ? 7.076 9.181 -1.883 1.00 85.61 15 A 1 ATOM 117 N N . SER A 1 16 ? 8.189 6.764 -5.676 1.00 93.45 16 A 1 ATOM 118 C CA . SER A 1 16 ? 9.485 6.110 -5.805 1.00 90.57 16 A 1 ATOM 119 C C . SER A 1 16 ? 9.338 4.714 -6.384 1.00 86.54 16 A 1 ATOM 120 O O . SER A 1 16 ? 9.974 3.774 -5.868 1.00 81.29 16 A 1 ATOM 121 C CB . SER A 1 16 ? 10.175 6.025 -4.445 1.00 86.38 16 A 1 ATOM 122 O OG . SER A 1 16 ? 10.337 7.296 -3.881 1.00 78.63 16 A 1 ATOM 123 O OXT . SER A 1 16 ? 8.585 4.529 -7.372 1.00 80.18 16 A 1 #