# 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_spkb23549 # _entry.id spkb23549 # 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 H15 N4 O2" 175.209 ARG y ARGININE C(C[C@@H](C(=O)O)N)CNC(=[NH2+])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" "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" "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 ARG 3 1 n LEU 4 1 n LEU 5 1 n LEU 6 1 n VAL 7 1 n LEU 8 1 n CYS 9 1 n TYR 10 1 n ILE 11 1 n THR 12 1 n LEU 13 1 n LEU 14 1 n ALA 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 @ 2025-07-09 10:07:31)" _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 93.97 _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 89.08 1 1 A LYS 2 2 87.43 1 2 A ARG 3 2 86.12 1 3 A LEU 4 2 95.96 1 4 A LEU 5 2 96.43 1 5 A LEU 6 2 96.44 1 6 A VAL 7 2 98.04 1 7 A LEU 8 2 96.65 1 8 A CYS 9 2 97.65 1 9 A TYR 10 2 95.29 1 10 A ILE 11 2 96.71 1 11 A THR 12 2 96.53 1 12 A LEU 13 2 94.03 1 13 A LEU 14 2 95.37 1 14 A ALA 15 2 92.20 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 ARG . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n VAL . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n CYS . 9 A 9 A 10 1 n TYR . 10 A 10 A 11 1 n ILE . 11 A 11 A 12 1 n THR . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n LEU . 14 A 14 A 15 1 n ALA . 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 ? -12.333 3.559 2.107 1.00 93.58 1 A 1 ATOM 2 C CA . MET A 1 1 ? -11.247 2.572 1.973 1.00 95.06 1 A 1 ATOM 3 C C . MET A 1 1 ? -10.108 2.877 2.944 1.00 95.55 1 A 1 ATOM 4 O O . MET A 1 1 ? -9.587 3.992 2.951 1.00 93.60 1 A 1 ATOM 5 C CB . MET A 1 1 ? -10.702 2.575 0.554 1.00 92.65 1 A 1 ATOM 6 C CG . MET A 1 1 ? -11.767 2.271 -0.490 1.00 87.03 1 A 1 ATOM 7 S SD . MET A 1 1 ? -12.459 0.648 -0.289 1.00 82.31 1 A 1 ATOM 8 C CE . MET A 1 1 ? -13.629 0.629 -1.628 1.00 72.85 1 A 1 ATOM 9 N N . LYS A 1 2 ? -9.746 1.897 3.773 1.00 93.22 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -8.675 2.070 4.755 1.00 94.51 2 A 1 ATOM 11 C C . LYS A 1 2 ? -7.606 0.989 4.607 1.00 95.56 2 A 1 ATOM 12 O O . LYS A 1 2 ? -6.413 1.278 4.669 1.00 93.53 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -9.242 2.046 6.178 1.00 92.53 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -10.016 3.303 6.565 1.00 85.84 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -11.437 3.294 6.033 1.00 84.07 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -12.184 4.553 6.425 1.00 77.71 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -13.558 4.555 5.911 1.00 69.87 2 A 1 ATOM 18 N N . ARG A 1 3 ? -8.047 -0.254 4.431 1.00 94.69 3 A 1 ATOM 19 C CA . ARG A 1 3 ? -7.117 -1.374 4.304 1.00 96.46 3 A 1 ATOM 20 C C . ARG A 1 3 ? -6.228 -1.226 3.074 1.00 97.57 3 A 1 ATOM 21 O O . ARG A 1 3 ? -5.035 -1.510 3.131 1.00 96.19 3 A 1 ATOM 22 C CB . ARG A 1 3 ? -7.870 -2.708 4.230 1.00 94.83 3 A 1 ATOM 23 C CG . ARG A 1 3 ? -8.321 -3.237 5.586 1.00 88.44 3 A 1 ATOM 24 C CD . ARG A 1 3 ? -9.604 -2.566 6.056 1.00 85.85 3 A 1 ATOM 25 N NE . ARG A 1 3 ? -10.102 -3.146 7.305 1.00 80.56 3 A 1 ATOM 26 C CZ . ARG A 1 3 ? -11.256 -2.828 7.861 1.00 75.53 3 A 1 ATOM 27 N NH1 . ARG A 1 3 ? -12.049 -1.934 7.307 1.00 70.10 3 A 1 ATOM 28 N NH2 . ARG A 1 3 ? -11.625 -3.413 8.986 1.00 67.05 3 A 1 ATOM 29 N N . LEU A 1 4 ? -6.814 -0.792 1.967 1.00 97.49 4 A 1 ATOM 30 C CA . LEU A 1 4 ? -6.070 -0.627 0.725 1.00 97.86 4 A 1 ATOM 31 C C . LEU A 1 4 ? -4.945 0.391 0.884 1.00 98.19 4 A 1 ATOM 32 O O . LEU A 1 4 ? -3.851 0.211 0.348 1.00 97.90 4 A 1 ATOM 33 C CB . LEU A 1 4 ? -7.014 -0.191 -0.401 1.00 97.86 4 A 1 ATOM 34 C CG . LEU A 1 4 ? -8.093 -1.206 -0.768 1.00 95.22 4 A 1 ATOM 35 C CD1 . LEU A 1 4 ? -9.032 -0.622 -1.811 1.00 91.19 4 A 1 ATOM 36 C CD2 . LEU A 1 4 ? -7.470 -2.492 -1.286 1.00 91.98 4 A 1 ATOM 37 N N . LEU A 1 5 ? -5.213 1.441 1.626 1.00 98.29 5 A 1 ATOM 38 C CA . LEU A 1 5 ? -4.213 2.474 1.873 1.00 98.37 5 A 1 ATOM 39 C C . LEU A 1 5 ? -3.042 1.911 2.669 1.00 98.44 5 A 1 ATOM 40 O O . LEU A 1 5 ? -1.888 2.274 2.437 1.00 98.28 5 A 1 ATOM 41 C CB . LEU A 1 5 ? -4.858 3.644 2.618 1.00 98.33 5 A 1 ATOM 42 C CG . LEU A 1 5 ? -3.981 4.885 2.679 1.00 95.61 5 A 1 ATOM 43 C CD1 . LEU A 1 5 ? -4.731 6.105 2.166 1.00 91.45 5 A 1 ATOM 44 C CD2 . LEU A 1 5 ? -3.516 5.141 4.108 1.00 92.69 5 A 1 ATOM 45 N N . LEU A 1 6 ? -3.339 1.014 3.592 1.00 98.47 6 A 1 ATOM 46 C CA . LEU A 1 6 ? -2.307 0.374 4.403 1.00 98.45 6 A 1 ATOM 47 C C . LEU A 1 6 ? -1.392 -0.479 3.532 1.00 98.47 6 A 1 ATOM 48 O O . LEU A 1 6 ? -0.173 -0.482 3.716 1.00 98.30 6 A 1 ATOM 49 C CB . LEU A 1 6 ? -2.964 -0.493 5.482 1.00 98.35 6 A 1 ATOM 50 C CG . LEU A 1 6 ? -2.001 -0.977 6.558 1.00 94.60 6 A 1 ATOM 51 C CD1 . LEU A 1 6 ? -1.668 0.160 7.522 1.00 91.57 6 A 1 ATOM 52 C CD2 . LEU A 1 6 ? -2.597 -2.145 7.328 1.00 93.33 6 A 1 ATOM 53 N N . VAL A 1 7 ? -1.983 -1.189 2.582 1.00 98.50 7 A 1 ATOM 54 C CA . VAL A 1 7 ? -1.218 -2.033 1.660 1.00 98.49 7 A 1 ATOM 55 C C . VAL A 1 7 ? -0.282 -1.177 0.813 1.00 98.55 7 A 1 ATOM 56 O O . VAL A 1 7 ? 0.888 -1.519 0.623 1.00 98.38 7 A 1 ATOM 57 C CB . VAL A 1 7 ? -2.157 -2.851 0.751 1.00 98.34 7 A 1 ATOM 58 C CG1 . VAL A 1 7 ? -1.365 -3.680 -0.249 1.00 97.07 7 A 1 ATOM 59 C CG2 . VAL A 1 7 ? -3.041 -3.766 1.588 1.00 96.96 7 A 1 ATOM 60 N N . LEU A 1 8 ? -0.801 -0.065 0.326 1.00 98.36 8 A 1 ATOM 61 C CA . LEU A 1 8 ? -0.004 0.851 -0.480 1.00 98.26 8 A 1 ATOM 62 C C . LEU A 1 8 ? 1.156 1.412 0.327 1.00 98.28 8 A 1 ATOM 63 O O . LEU A 1 8 ? 2.271 1.542 -0.172 1.00 98.09 8 A 1 ATOM 64 C CB . LEU A 1 8 ? -0.886 1.992 -1.007 1.00 98.12 8 A 1 ATOM 65 C CG . LEU A 1 8 ? -1.248 1.911 -2.489 1.00 94.71 8 A 1 ATOM 66 C CD1 . LEU A 1 8 ? 0.003 2.030 -3.346 1.00 93.07 8 A 1 ATOM 67 C CD2 . LEU A 1 8 ? -1.976 0.613 -2.793 1.00 94.32 8 A 1 ATOM 68 N N . CYS A 1 9 ? 0.890 1.728 1.570 1.00 98.28 9 A 1 ATOM 69 C CA . CYS A 1 9 ? 1.916 2.247 2.463 1.00 98.26 9 A 1 ATOM 70 C C . CYS A 1 9 ? 3.029 1.223 2.667 1.00 98.28 9 A 1 ATOM 71 O O . CYS A 1 9 ? 4.209 1.570 2.699 1.00 98.04 9 A 1 ATOM 72 C CB . CYS A 1 9 ? 1.289 2.624 3.806 1.00 98.07 9 A 1 ATOM 73 S SG . CYS A 1 9 ? 2.441 3.487 4.879 1.00 94.99 9 A 1 ATOM 74 N N . TYR A 1 10 ? 2.637 -0.036 2.789 1.00 97.86 10 A 1 ATOM 75 C CA . TYR A 1 10 ? 3.594 -1.126 2.969 1.00 97.85 10 A 1 ATOM 76 C C . TYR A 1 10 ? 4.497 -1.270 1.748 1.00 97.99 10 A 1 ATOM 77 O O . TYR A 1 10 ? 5.719 -1.367 1.874 1.00 97.60 10 A 1 ATOM 78 C CB . TYR A 1 10 ? 2.838 -2.434 3.230 1.00 97.61 10 A 1 ATOM 79 C CG . TYR A 1 10 ? 3.749 -3.627 3.399 1.00 95.36 10 A 1 ATOM 80 C CD1 . TYR A 1 10 ? 3.972 -4.505 2.343 1.00 93.12 10 A 1 ATOM 81 C CD2 . TYR A 1 10 ? 4.388 -3.860 4.609 1.00 93.84 10 A 1 ATOM 82 C CE1 . TYR A 1 10 ? 4.813 -5.599 2.495 1.00 92.82 10 A 1 ATOM 83 C CE2 . TYR A 1 10 ? 5.234 -4.956 4.764 1.00 93.30 10 A 1 ATOM 84 C CZ . TYR A 1 10 ? 5.440 -5.819 3.705 1.00 94.00 10 A 1 ATOM 85 O OH . TYR A 1 10 ? 6.277 -6.898 3.854 1.00 92.17 10 A 1 ATOM 86 N N . ILE A 1 11 ? 3.884 -1.280 0.569 1.00 97.87 11 A 1 ATOM 87 C CA . ILE A 1 11 ? 4.630 -1.404 -0.680 1.00 97.74 11 A 1 ATOM 88 C C . ILE A 1 11 ? 5.554 -0.207 -0.874 1.00 97.85 11 A 1 ATOM 89 O O . ILE A 1 11 ? 6.701 -0.357 -1.299 1.00 97.32 11 A 1 ATOM 90 C CB . ILE A 1 11 ? 3.667 -1.536 -1.874 1.00 97.48 11 A 1 ATOM 91 C CG1 . ILE A 1 11 ? 2.855 -2.831 -1.755 1.00 96.07 11 A 1 ATOM 92 C CG2 . ILE A 1 11 ? 4.448 -1.526 -3.189 1.00 95.87 11 A 1 ATOM 93 C CD1 . ILE A 1 11 ? 1.704 -2.907 -2.721 1.00 93.48 11 A 1 ATOM 94 N N . THR A 1 12 ? 5.059 0.959 -0.556 1.00 98.16 12 A 1 ATOM 95 C CA . THR A 1 12 ? 5.843 2.185 -0.678 1.00 98.04 12 A 1 ATOM 96 C C . THR A 1 12 ? 7.057 2.142 0.243 1.00 98.07 12 A 1 ATOM 97 O O . THR A 1 12 ? 8.138 2.608 -0.116 1.00 97.27 12 A 1 ATOM 98 C CB . THR A 1 12 ? 4.986 3.410 -0.339 1.00 97.50 12 A 1 ATOM 99 O OG1 . THR A 1 12 ? 3.847 3.452 -1.187 1.00 93.83 12 A 1 ATOM 100 C CG2 . THR A 1 12 ? 5.780 4.696 -0.527 1.00 92.82 12 A 1 ATOM 101 N N . LEU A 1 13 ? 6.875 1.586 1.416 1.00 97.46 13 A 1 ATOM 102 C CA . LEU A 1 13 ? 7.959 1.466 2.386 1.00 97.27 13 A 1 ATOM 103 C C . LEU A 1 13 ? 9.038 0.515 1.879 1.00 97.55 13 A 1 ATOM 104 O O . LEU A 1 13 ? 10.232 0.745 2.095 1.00 96.54 13 A 1 ATOM 105 C CB . LEU A 1 13 ? 7.401 0.974 3.725 1.00 96.50 13 A 1 ATOM 106 C CG . LEU A 1 13 ? 8.398 1.029 4.881 1.00 91.85 13 A 1 ATOM 107 C CD1 . LEU A 1 13 ? 8.669 2.477 5.284 1.00 87.62 13 A 1 ATOM 108 C CD2 . LEU A 1 13 ? 7.875 0.246 6.070 1.00 87.45 13 A 1 ATOM 109 N N . LEU A 1 14 ? 8.624 -0.551 1.201 1.00 97.71 14 A 1 ATOM 110 C CA . LEU A 1 14 ? 9.551 -1.532 0.642 1.00 97.47 14 A 1 ATOM 111 C C . LEU A 1 14 ? 10.337 -0.954 -0.524 1.00 97.65 14 A 1 ATOM 112 O O . LEU A 1 14 ? 11.536 -1.213 -0.666 1.00 96.78 14 A 1 ATOM 113 C CB . LEU A 1 14 ? 8.780 -2.772 0.184 1.00 96.84 14 A 1 ATOM 114 C CG . LEU A 1 14 ? 8.095 -3.552 1.306 1.00 94.22 14 A 1 ATOM 115 C CD1 . LEU A 1 14 ? 7.271 -4.684 0.712 1.00 91.59 14 A 1 ATOM 116 C CD2 . LEU A 1 14 ? 9.122 -4.098 2.290 1.00 90.67 14 A 1 ATOM 117 N N . ALA A 1 15 ? 9.648 -0.189 -1.357 1.00 96.08 15 A 1 ATOM 118 C CA . ALA A 1 15 ? 10.264 0.409 -2.531 1.00 95.07 15 A 1 ATOM 119 C C . ALA A 1 15 ? 10.921 1.742 -2.183 1.00 94.30 15 A 1 ATOM 120 O O . ALA A 1 15 ? 10.290 2.552 -1.481 1.00 92.06 15 A 1 ATOM 121 C CB . ALA A 1 15 ? 9.238 0.588 -3.637 1.00 92.56 15 A 1 ATOM 122 O OXT . ALA A 1 15 ? 12.049 1.983 -2.614 1.00 83.15 15 A 1 #