# 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_spkb42374 # _entry.id spkb42374 # 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" "C5 H9 N O2" 115.130 PRO y PROLINE C1C[C@H](NC1)C(=O)O ? "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" "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 TYR 3 1 n LYS 4 1 n LEU 5 1 n LEU 6 1 n PRO 7 1 n CYS 8 1 n LEU 9 1 n LEU 10 1 n ALA 11 1 n ILE 12 1 n LEU 13 1 n LEU 14 1 n THR 15 1 n GLY 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 @ 2025-07-07 16:24:54)" _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 90.62 _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 83.93 1 1 A LYS 2 2 82.53 1 2 A TYR 3 2 85.80 1 3 A LYS 4 2 86.09 1 4 A LEU 5 2 92.06 1 5 A LEU 6 2 91.96 1 6 A PRO 7 2 94.99 1 7 A CYS 8 2 94.31 1 8 A LEU 9 2 93.67 1 9 A LEU 10 2 94.19 1 10 A ALA 11 2 96.14 1 11 A ILE 12 2 95.06 1 12 A LEU 13 2 95.02 1 13 A LEU 14 2 95.07 1 14 A THR 15 2 91.15 1 15 A GLY 16 2 82.62 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 TYR . 3 A 3 A 4 1 n LYS . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n PRO . 7 A 7 A 8 1 n CYS . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n ILE . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n THR . 15 A 15 A 16 1 n GLY . 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 ? 2.504 11.505 -2.481 1.00 89.27 1 A 1 ATOM 2 C CA . MET A 1 1 ? 1.306 10.782 -2.944 1.00 90.80 1 A 1 ATOM 3 C C . MET A 1 1 ? 0.492 10.235 -1.774 1.00 91.14 1 A 1 ATOM 4 O O . MET A 1 1 ? -0.712 10.060 -1.879 1.00 89.02 1 A 1 ATOM 5 C CB . MET A 1 1 ? 1.716 9.615 -3.843 1.00 87.19 1 A 1 ATOM 6 C CG . MET A 1 1 ? 2.417 10.103 -5.105 1.00 80.28 1 A 1 ATOM 7 S SD . MET A 1 1 ? 1.280 10.949 -6.193 1.00 75.94 1 A 1 ATOM 8 C CE . MET A 1 1 ? 2.429 11.634 -7.368 1.00 67.77 1 A 1 ATOM 9 N N . LYS A 1 2 ? 1.164 9.977 -0.679 1.00 89.09 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 0.486 9.486 0.530 1.00 90.16 2 A 1 ATOM 11 C C . LYS A 1 2 ? -0.223 8.153 0.256 1.00 90.16 2 A 1 ATOM 12 O O . LYS A 1 2 ? -1.330 7.915 0.731 1.00 89.33 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -0.512 10.552 0.991 1.00 88.20 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -0.838 10.434 2.462 1.00 80.55 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -1.682 11.620 2.900 1.00 78.74 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -2.142 11.446 4.333 1.00 72.16 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -2.837 12.680 4.794 1.00 64.40 2 A 1 ATOM 18 N N . TYR A 1 3 ? 0.403 7.306 -0.503 1.00 89.01 3 A 1 ATOM 19 C CA . TYR A 1 3 ? -0.180 6.010 -0.869 1.00 90.26 3 A 1 ATOM 20 C C . TYR A 1 3 ? 0.452 4.860 -0.080 1.00 91.71 3 A 1 ATOM 21 O O . TYR A 1 3 ? -0.005 3.726 -0.165 1.00 90.21 3 A 1 ATOM 22 C CB . TYR A 1 3 ? 0.025 5.780 -2.372 1.00 89.20 3 A 1 ATOM 23 C CG . TYR A 1 3 ? 1.462 5.438 -2.721 1.00 84.22 3 A 1 ATOM 24 C CD1 . TYR A 1 3 ? 2.476 6.386 -2.612 1.00 83.72 3 A 1 ATOM 25 C CD2 . TYR A 1 3 ? 1.788 4.157 -3.148 1.00 83.01 3 A 1 ATOM 26 C CE1 . TYR A 1 3 ? 3.791 6.067 -2.926 1.00 80.95 3 A 1 ATOM 27 C CE2 . TYR A 1 3 ? 3.109 3.830 -3.469 1.00 83.15 3 A 1 ATOM 28 C CZ . TYR A 1 3 ? 4.102 4.790 -3.359 1.00 83.14 3 A 1 ATOM 29 O OH . TYR A 1 3 ? 5.401 4.465 -3.668 1.00 80.96 3 A 1 ATOM 30 N N . LYS A 1 4 ? 1.494 5.156 0.663 1.00 92.88 4 A 1 ATOM 31 C CA . LYS A 1 4 ? 2.198 4.142 1.449 1.00 93.94 4 A 1 ATOM 32 C C . LYS A 1 4 ? 1.476 3.888 2.775 1.00 94.92 4 A 1 ATOM 33 O O . LYS A 1 4 ? 2.072 3.970 3.848 1.00 93.94 4 A 1 ATOM 34 C CB . LYS A 1 4 ? 3.635 4.611 1.703 1.00 93.09 4 A 1 ATOM 35 C CG . LYS A 1 4 ? 4.446 4.721 0.421 1.00 85.15 4 A 1 ATOM 36 C CD . LYS A 1 4 ? 5.111 3.392 0.089 1.00 81.30 4 A 1 ATOM 37 C CE . LYS A 1 4 ? 6.041 3.535 -1.103 1.00 74.07 4 A 1 ATOM 38 N NZ . LYS A 1 4 ? 6.996 2.403 -1.185 1.00 65.55 4 A 1 ATOM 39 N N . LEU A 1 5 ? 0.210 3.587 2.679 1.00 94.66 5 A 1 ATOM 40 C CA . LEU A 1 5 ? -0.601 3.338 3.863 1.00 95.33 5 A 1 ATOM 41 C C . LEU A 1 5 ? -1.012 1.867 3.927 1.00 95.73 5 A 1 ATOM 42 O O . LEU A 1 5 ? -0.441 1.019 3.246 1.00 95.01 5 A 1 ATOM 43 C CB . LEU A 1 5 ? -1.832 4.252 3.812 1.00 95.16 5 A 1 ATOM 44 C CG . LEU A 1 5 ? -1.489 5.738 3.870 1.00 90.10 5 A 1 ATOM 45 C CD1 . LEU A 1 5 ? -2.597 6.554 3.220 1.00 85.27 5 A 1 ATOM 46 C CD2 . LEU A 1 5 ? -1.307 6.181 5.318 1.00 85.24 5 A 1 ATOM 47 N N . LEU A 1 6 ? -2.010 1.592 4.732 1.00 95.69 6 A 1 ATOM 48 C CA . LEU A 1 6 ? -2.507 0.222 4.876 1.00 95.56 6 A 1 ATOM 49 C C . LEU A 1 6 ? -2.950 -0.379 3.541 1.00 95.89 6 A 1 ATOM 50 O O . LEU A 1 6 ? -2.657 -1.544 3.268 1.00 95.62 6 A 1 ATOM 51 C CB . LEU A 1 6 ? -3.673 0.224 5.865 1.00 95.14 6 A 1 ATOM 52 C CG . LEU A 1 6 ? -3.217 0.318 7.316 1.00 89.25 6 A 1 ATOM 53 C CD1 . LEU A 1 6 ? -4.185 1.151 8.126 1.00 84.06 6 A 1 ATOM 54 C CD2 . LEU A 1 6 ? -3.104 -1.081 7.908 1.00 84.44 6 A 1 ATOM 55 N N . PRO A 1 7 ? -3.657 0.392 2.724 1.00 95.43 7 A 1 ATOM 56 C CA . PRO A 1 7 ? -4.118 -0.126 1.424 1.00 95.63 7 A 1 ATOM 57 C C . PRO A 1 7 ? -2.965 -0.604 0.552 1.00 95.94 7 A 1 ATOM 58 O O . PRO A 1 7 ? -3.117 -1.525 -0.246 1.00 95.26 7 A 1 ATOM 59 C CB . PRO A 1 7 ? -4.828 1.077 0.791 1.00 94.52 7 A 1 ATOM 60 C CG . PRO A 1 7 ? -4.373 2.256 1.565 1.00 93.27 7 A 1 ATOM 61 C CD . PRO A 1 7 ? -4.098 1.760 2.947 1.00 94.85 7 A 1 ATOM 62 N N . CYS A 1 8 ? -1.818 0.015 0.706 1.00 95.21 8 A 1 ATOM 63 C CA . CYS A 1 8 ? -0.639 -0.362 -0.076 1.00 95.36 8 A 1 ATOM 64 C C . CYS A 1 8 ? -0.171 -1.761 0.331 1.00 95.91 8 A 1 ATOM 65 O O . CYS A 1 8 ? 0.251 -2.554 -0.504 1.00 95.28 8 A 1 ATOM 66 C CB . CYS A 1 8 ? 0.475 0.655 0.161 1.00 94.62 8 A 1 ATOM 67 S SG . CYS A 1 8 ? 1.773 0.530 -1.072 1.00 89.47 8 A 1 ATOM 68 N N . LEU A 1 9 ? -0.253 -2.046 1.611 1.00 94.90 9 A 1 ATOM 69 C CA . LEU A 1 9 ? 0.147 -3.354 2.123 1.00 95.38 9 A 1 ATOM 70 C C . LEU A 1 9 ? -0.738 -4.453 1.544 1.00 96.18 9 A 1 ATOM 71 O O . LEU A 1 9 ? -0.249 -5.525 1.188 1.00 96.28 9 A 1 ATOM 72 C CB . LEU A 1 9 ? 0.037 -3.347 3.647 1.00 95.40 9 A 1 ATOM 73 C CG . LEU A 1 9 ? 0.971 -4.354 4.308 1.00 92.46 9 A 1 ATOM 74 C CD1 . LEU A 1 9 ? 2.372 -3.758 4.433 1.00 88.64 9 A 1 ATOM 75 C CD2 . LEU A 1 9 ? 0.450 -4.732 5.685 1.00 90.08 9 A 1 ATOM 76 N N . LEU A 1 10 ? -2.014 -4.184 1.455 1.00 96.06 10 A 1 ATOM 77 C CA . LEU A 1 10 ? -2.963 -5.151 0.900 1.00 95.91 10 A 1 ATOM 78 C C . LEU A 1 10 ? -2.657 -5.420 -0.566 1.00 96.34 10 A 1 ATOM 79 O O . LEU A 1 10 ? -2.749 -6.558 -1.031 1.00 96.39 10 A 1 ATOM 80 C CB . LEU A 1 10 ? -4.383 -4.601 1.051 1.00 95.68 10 A 1 ATOM 81 C CG . LEU A 1 10 ? -5.099 -5.157 2.276 1.00 92.78 10 A 1 ATOM 82 C CD1 . LEU A 1 10 ? -6.191 -4.210 2.734 1.00 89.15 10 A 1 ATOM 83 C CD2 . LEU A 1 10 ? -5.697 -6.522 1.943 1.00 91.18 10 A 1 ATOM 84 N N . ALA A 1 11 ? -2.301 -4.381 -1.278 1.00 96.46 11 A 1 ATOM 85 C CA . ALA A 1 11 ? -1.980 -4.501 -2.701 1.00 96.33 11 A 1 ATOM 86 C C . ALA A 1 11 ? -0.732 -5.361 -2.896 1.00 96.73 11 A 1 ATOM 87 O O . ALA A 1 11 ? -0.650 -6.150 -3.833 1.00 95.67 11 A 1 ATOM 88 C CB . ALA A 1 11 ? -1.761 -3.114 -3.288 1.00 95.52 11 A 1 ATOM 89 N N . ILE A 1 12 ? 0.228 -5.205 -2.014 1.00 96.51 12 A 1 ATOM 90 C CA . ILE A 1 12 ? 1.469 -5.973 -2.094 1.00 96.35 12 A 1 ATOM 91 C C . ILE A 1 12 ? 1.189 -7.458 -1.864 1.00 96.87 12 A 1 ATOM 92 O O . ILE A 1 12 ? 1.741 -8.320 -2.553 1.00 96.17 12 A 1 ATOM 93 C CB . ILE A 1 12 ? 2.481 -5.451 -1.049 1.00 95.88 12 A 1 ATOM 94 C CG1 . ILE A 1 12 ? 2.915 -4.019 -1.380 1.00 94.25 12 A 1 ATOM 95 C CG2 . ILE A 1 12 ? 3.716 -6.358 -1.020 1.00 93.75 12 A 1 ATOM 96 C CD1 . ILE A 1 12 ? 3.431 -3.274 -0.157 1.00 90.67 12 A 1 ATOM 97 N N . LEU A 1 13 ? 0.336 -7.747 -0.908 1.00 96.79 13 A 1 ATOM 98 C CA . LEU A 1 13 ? -0.020 -9.128 -0.592 1.00 96.74 13 A 1 ATOM 99 C C . LEU A 1 13 ? -0.780 -9.773 -1.745 1.00 97.11 13 A 1 ATOM 100 O O . LEU A 1 13 ? -0.627 -10.965 -2.012 1.00 96.65 13 A 1 ATOM 101 C CB . LEU A 1 13 ? -0.867 -9.153 0.691 1.00 96.43 13 A 1 ATOM 102 C CG . LEU A 1 13 ? -0.073 -9.446 1.970 1.00 94.46 13 A 1 ATOM 103 C CD1 . LEU A 1 13 ? 0.437 -10.879 1.944 1.00 90.16 13 A 1 ATOM 104 C CD2 . LEU A 1 13 ? 1.085 -8.489 2.130 1.00 91.81 13 A 1 ATOM 105 N N . LEU A 1 14 ? -1.600 -8.985 -2.401 1.00 97.18 14 A 1 ATOM 106 C CA . LEU A 1 14 ? -2.400 -9.479 -3.523 1.00 97.00 14 A 1 ATOM 107 C C . LEU A 1 14 ? -1.533 -9.676 -4.762 1.00 96.92 14 A 1 ATOM 108 O O . LEU A 1 14 ? -1.656 -10.675 -5.470 1.00 95.93 14 A 1 ATOM 109 C CB . LEU A 1 14 ? -3.528 -8.480 -3.810 1.00 96.67 14 A 1 ATOM 110 C CG . LEU A 1 14 ? -4.888 -9.146 -3.993 1.00 95.32 14 A 1 ATOM 111 C CD1 . LEU A 1 14 ? -6.002 -8.142 -3.730 1.00 90.32 14 A 1 ATOM 112 C CD2 . LEU A 1 14 ? -5.027 -9.725 -5.386 1.00 91.21 14 A 1 ATOM 113 N N . THR A 1 15 ? -0.673 -8.737 -5.034 1.00 96.24 15 A 1 ATOM 114 C CA . THR A 1 15 ? 0.207 -8.814 -6.203 1.00 95.40 15 A 1 ATOM 115 C C . THR A 1 15 ? 1.315 -9.840 -5.993 1.00 94.52 15 A 1 ATOM 116 O O . THR A 1 15 ? 1.846 -10.390 -6.960 1.00 88.52 15 A 1 ATOM 117 C CB . THR A 1 15 ? 0.835 -7.441 -6.484 1.00 93.17 15 A 1 ATOM 118 O OG1 . THR A 1 15 ? 1.340 -6.883 -5.285 1.00 85.48 15 A 1 ATOM 119 C CG2 . THR A 1 15 ? -0.173 -6.487 -7.096 1.00 84.72 15 A 1 ATOM 120 N N . GLY A 1 16 ? 1.665 -10.074 -4.751 1.00 89.71 16 A 1 ATOM 121 C CA . GLY A 1 16 ? 2.701 -11.055 -4.429 1.00 86.28 16 A 1 ATOM 122 C C . GLY A 1 16 ? 2.257 -12.470 -4.721 1.00 81.80 16 A 1 ATOM 123 O O . GLY A 1 16 ? 2.828 -13.104 -5.621 1.00 74.57 16 A 1 ATOM 124 O OXT . GLY A 1 16 ? 1.374 -12.948 -4.037 1.00 80.76 16 A 1 #