# 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_spkb23546 # _entry.id spkb23546 # 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" "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 LYS 3 1 n ILE 4 1 n LEU 5 1 n ALA 6 1 n LEU 7 1 n LEU 8 1 n VAL 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 @ 2025-07-09 12:26:18)" _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 95.74 _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 92.89 1 1 A LYS 2 2 92.35 1 2 A LYS 3 2 94.13 1 3 A ILE 4 2 97.36 1 4 A LEU 5 2 96.28 1 5 A ALA 6 2 98.33 1 6 A LEU 7 2 97.12 1 7 A LEU 8 2 97.34 1 8 A VAL 9 2 97.95 1 9 A ILE 10 2 97.40 1 10 A ALA 11 2 98.27 1 11 A PRO 12 2 98.06 1 12 A LEU 13 2 96.21 1 13 A LEU 14 2 95.44 1 14 A ILE 15 2 96.17 1 15 A SER 16 2 88.69 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 ILE . 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 LEU . 8 A 8 A 9 1 n VAL . 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 ? 6.521 13.558 4.630 1.00 97.14 1 A 1 ATOM 2 C CA . MET A 1 1 ? 5.792 12.726 5.621 1.00 97.58 1 A 1 ATOM 3 C C . MET A 1 1 ? 5.877 11.244 5.259 1.00 97.58 1 A 1 ATOM 4 O O . MET A 1 1 ? 5.792 10.880 4.092 1.00 96.87 1 A 1 ATOM 5 C CB . MET A 1 1 ? 4.325 13.141 5.673 1.00 96.07 1 A 1 ATOM 6 C CG . MET A 1 1 ? 4.133 14.447 6.443 1.00 90.85 1 A 1 ATOM 7 S SD . MET A 1 1 ? 4.689 15.867 5.509 1.00 87.84 1 A 1 ATOM 8 C CE . MET A 1 1 ? 4.416 17.163 6.710 1.00 79.21 1 A 1 ATOM 9 N N . LYS A 1 2 ? 6.033 10.386 6.256 1.00 97.38 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 6.126 8.940 6.049 1.00 97.89 2 A 1 ATOM 11 C C . LYS A 1 2 ? 4.756 8.269 6.137 1.00 98.16 2 A 1 ATOM 12 O O . LYS A 1 2 ? 4.619 7.089 5.811 1.00 97.54 2 A 1 ATOM 13 C CB . LYS A 1 2 ? 7.062 8.332 7.097 1.00 97.09 2 A 1 ATOM 14 C CG . LYS A 1 2 ? 8.515 8.706 6.884 1.00 92.08 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 9.351 8.395 8.108 1.00 90.08 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 10.779 8.873 7.942 1.00 83.82 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 11.571 7.946 7.104 1.00 77.07 2 A 1 ATOM 18 N N . LYS A 1 3 ? 3.754 9.021 6.579 1.00 98.14 3 A 1 ATOM 19 C CA . LYS A 1 3 ? 2.397 8.490 6.714 1.00 98.39 3 A 1 ATOM 20 C C . LYS A 1 3 ? 1.805 8.172 5.347 1.00 98.50 3 A 1 ATOM 21 O O . LYS A 1 3 ? 1.153 7.148 5.166 1.00 98.09 3 A 1 ATOM 22 C CB . LYS A 1 3 ? 1.516 9.497 7.459 1.00 98.08 3 A 1 ATOM 23 C CG . LYS A 1 3 ? 1.888 9.617 8.929 1.00 95.24 3 A 1 ATOM 24 C CD . LYS A 1 3 ? 1.472 8.391 9.716 1.00 92.06 3 A 1 ATOM 25 C CE . LYS A 1 3 ? 2.345 8.179 10.935 1.00 87.77 3 A 1 ATOM 26 N NZ . LYS A 1 3 ? 2.058 6.877 11.578 1.00 80.88 3 A 1 ATOM 27 N N . ILE A 1 4 ? 2.035 9.051 4.390 1.00 98.14 4 A 1 ATOM 28 C CA . ILE A 1 4 ? 1.524 8.853 3.036 1.00 98.18 4 A 1 ATOM 29 C C . ILE A 1 4 ? 2.188 7.641 2.393 1.00 98.24 4 A 1 ATOM 30 O O . ILE A 1 4 ? 1.556 6.886 1.656 1.00 97.89 4 A 1 ATOM 31 C CB . ILE A 1 4 ? 1.766 10.107 2.175 1.00 98.24 4 A 1 ATOM 32 C CG1 . ILE A 1 4 ? 1.039 11.317 2.770 1.00 97.16 4 A 1 ATOM 33 C CG2 . ILE A 1 4 ? 1.279 9.863 0.744 1.00 96.60 4 A 1 ATOM 34 C CD1 . ILE A 1 4 ? 1.506 12.625 2.166 1.00 94.46 4 A 1 ATOM 35 N N . LEU A 1 5 ? 3.448 7.452 2.668 1.00 98.30 5 A 1 ATOM 36 C CA . LEU A 1 5 ? 4.198 6.325 2.127 1.00 98.17 5 A 1 ATOM 37 C C . LEU A 1 5 ? 3.684 5.009 2.699 1.00 98.22 5 A 1 ATOM 38 O O . LEU A 1 5 ? 3.570 4.016 1.984 1.00 98.11 5 A 1 ATOM 39 C CB . LEU A 1 5 ? 5.680 6.488 2.452 1.00 98.00 5 A 1 ATOM 40 C CG . LEU A 1 5 ? 6.592 5.722 1.503 1.00 94.49 5 A 1 ATOM 41 C CD1 . LEU A 1 5 ? 6.753 6.481 0.193 1.00 92.26 5 A 1 ATOM 42 C CD2 . LEU A 1 5 ? 7.953 5.490 2.140 1.00 92.67 5 A 1 ATOM 43 N N . ALA A 1 6 ? 3.385 5.003 3.981 1.00 98.45 6 A 1 ATOM 44 C CA . ALA A 1 6 ? 2.875 3.813 4.657 1.00 98.39 6 A 1 ATOM 45 C C . ALA A 1 6 ? 1.502 3.424 4.118 1.00 98.48 6 A 1 ATOM 46 O O . ALA A 1 6 ? 1.222 2.250 3.891 1.00 98.16 6 A 1 ATOM 47 C CB . ALA A 1 6 ? 2.789 4.071 6.156 1.00 98.15 6 A 1 ATOM 48 N N . LEU A 1 7 ? 0.646 4.424 3.906 1.00 98.55 7 A 1 ATOM 49 C CA . LEU A 1 7 ? -0.701 4.187 3.388 1.00 98.57 7 A 1 ATOM 50 C C . LEU A 1 7 ? -0.644 3.707 1.942 1.00 98.66 7 A 1 ATOM 51 O O . LEU A 1 7 ? -1.490 2.927 1.508 1.00 98.47 7 A 1 ATOM 52 C CB . LEU A 1 7 ? -1.521 5.476 3.476 1.00 98.42 7 A 1 ATOM 53 C CG . LEU A 1 7 ? -2.033 5.790 4.881 1.00 96.27 7 A 1 ATOM 54 C CD1 . LEU A 1 7 ? -2.332 7.271 5.030 1.00 93.63 7 A 1 ATOM 55 C CD2 . LEU A 1 7 ? -3.288 4.975 5.177 1.00 94.39 7 A 1 ATOM 56 N N . LEU A 1 8 ? 0.337 4.166 1.205 1.00 98.65 8 A 1 ATOM 57 C CA . LEU A 1 8 ? 0.502 3.795 -0.199 1.00 98.62 8 A 1 ATOM 58 C C . LEU A 1 8 ? 1.001 2.360 -0.341 1.00 98.68 8 A 1 ATOM 59 O O . LEU A 1 8 ? 0.917 1.772 -1.414 1.00 98.47 8 A 1 ATOM 60 C CB . LEU A 1 8 ? 1.478 4.766 -0.868 1.00 98.48 8 A 1 ATOM 61 C CG . LEU A 1 8 ? 0.931 5.415 -2.135 1.00 96.35 8 A 1 ATOM 62 C CD1 . LEU A 1 8 ? 1.737 6.664 -2.483 1.00 94.32 8 A 1 ATOM 63 C CD2 . LEU A 1 8 ? 0.966 4.443 -3.296 1.00 95.17 8 A 1 ATOM 64 N N . VAL A 1 9 ? 1.518 1.799 0.728 1.00 98.61 9 A 1 ATOM 65 C CA . VAL A 1 9 ? 2.026 0.430 0.715 1.00 98.54 9 A 1 ATOM 66 C C . VAL A 1 9 ? 0.952 -0.563 1.155 1.00 98.62 9 A 1 ATOM 67 O O . VAL A 1 9 ? 0.956 -1.721 0.735 1.00 98.35 9 A 1 ATOM 68 C CB . VAL A 1 9 ? 3.255 0.303 1.627 1.00 98.19 9 A 1 ATOM 69 C CG1 . VAL A 1 9 ? 3.792 -1.114 1.615 1.00 96.55 9 A 1 ATOM 70 C CG2 . VAL A 1 9 ? 4.341 1.270 1.190 1.00 96.82 9 A 1 ATOM 71 N N . ILE A 1 10 ? 0.043 -0.112 1.994 1.00 98.51 10 A 1 ATOM 72 C CA . ILE A 1 10 ? -1.021 -0.973 2.505 1.00 98.45 10 A 1 ATOM 73 C C . ILE A 1 10 ? -2.047 -1.283 1.425 1.00 98.53 10 A 1 ATOM 74 O O . ILE A 1 10 ? -2.481 -2.419 1.268 1.00 98.28 10 A 1 ATOM 75 C CB . ILE A 1 10 ? -1.721 -0.318 3.712 1.00 98.18 10 A 1 ATOM 76 C CG1 . ILE A 1 10 ? -0.703 0.001 4.817 1.00 96.37 10 A 1 ATOM 77 C CG2 . ILE A 1 10 ? -2.816 -1.237 4.253 1.00 96.08 10 A 1 ATOM 78 C CD1 . ILE A 1 10 ? -0.064 -1.240 5.415 1.00 94.83 10 A 1 ATOM 79 N N . ALA A 1 11 ? -2.459 -0.258 0.690 1.00 98.44 11 A 1 ATOM 80 C CA . ALA A 1 11 ? -3.465 -0.418 -0.361 1.00 98.40 11 A 1 ATOM 81 C C . ALA A 1 11 ? -3.014 -1.382 -1.465 1.00 98.50 11 A 1 ATOM 82 O O . ALA A 1 11 ? -3.708 -2.358 -1.751 1.00 98.00 11 A 1 ATOM 83 C CB . ALA A 1 11 ? -3.835 0.942 -0.939 1.00 98.02 11 A 1 ATOM 84 N N . PRO A 1 12 ? -1.875 -1.130 -2.098 1.00 98.49 12 A 1 ATOM 85 C CA . PRO A 1 12 ? -1.373 -1.997 -3.174 1.00 98.35 12 A 1 ATOM 86 C C . PRO A 1 12 ? -0.982 -3.386 -2.691 1.00 98.44 12 A 1 ATOM 87 O O . PRO A 1 12 ? -1.018 -4.343 -3.457 1.00 97.91 12 A 1 ATOM 88 C CB . PRO A 1 12 ? -0.153 -1.239 -3.703 1.00 97.82 12 A 1 ATOM 89 C CG . PRO A 1 12 ? 0.266 -0.354 -2.595 1.00 97.15 12 A 1 ATOM 90 C CD . PRO A 1 12 ? -0.995 0.017 -1.866 1.00 98.28 12 A 1 ATOM 91 N N . LEU A 1 13 ? -0.614 -3.514 -1.451 1.00 98.11 13 A 1 ATOM 92 C CA . LEU A 1 13 ? -0.218 -4.799 -0.873 1.00 98.14 13 A 1 ATOM 93 C C . LEU A 1 13 ? -1.425 -5.713 -0.709 1.00 98.33 13 A 1 ATOM 94 O O . LEU A 1 13 ? -1.313 -6.930 -0.853 1.00 97.52 13 A 1 ATOM 95 C CB . LEU A 1 13 ? 0.446 -4.574 0.486 1.00 97.75 13 A 1 ATOM 96 C CG . LEU A 1 13 ? 1.270 -5.769 0.946 1.00 94.89 13 A 1 ATOM 97 C CD1 . LEU A 1 13 ? 2.756 -5.464 0.834 1.00 92.67 13 A 1 ATOM 98 C CD2 . LEU A 1 13 ? 0.926 -6.139 2.377 1.00 92.29 13 A 1 ATOM 99 N N . LEU A 1 14 ? -2.579 -5.136 -0.405 1.00 97.35 14 A 1 ATOM 100 C CA . LEU A 1 14 ? -3.807 -5.906 -0.209 1.00 97.45 14 A 1 ATOM 101 C C . LEU A 1 14 ? -4.366 -6.409 -1.534 1.00 97.60 14 A 1 ATOM 102 O O . LEU A 1 14 ? -4.752 -7.572 -1.648 1.00 96.68 14 A 1 ATOM 103 C CB . LEU A 1 14 ? -4.853 -5.043 0.498 1.00 97.11 14 A 1 ATOM 104 C CG . LEU A 1 14 ? -6.046 -5.831 1.022 1.00 94.95 14 A 1 ATOM 105 C CD1 . LEU A 1 14 ? -5.666 -6.562 2.305 1.00 91.53 14 A 1 ATOM 106 C CD2 . LEU A 1 14 ? -7.223 -4.909 1.280 1.00 90.85 14 A 1 ATOM 107 N N . ILE A 1 15 ? -4.432 -5.550 -2.526 1.00 97.93 15 A 1 ATOM 108 C CA . ILE A 1 15 ? -4.948 -5.909 -3.847 1.00 97.83 15 A 1 ATOM 109 C C . ILE A 1 15 ? -3.998 -6.835 -4.595 1.00 97.81 15 A 1 ATOM 110 O O . ILE A 1 15 ? -4.427 -7.677 -5.380 1.00 97.17 15 A 1 ATOM 111 C CB . ILE A 1 15 ? -5.214 -4.652 -4.684 1.00 97.41 15 A 1 ATOM 112 C CG1 . ILE A 1 15 ? -4.014 -3.709 -4.647 1.00 95.38 15 A 1 ATOM 113 C CG2 . ILE A 1 15 ? -6.464 -3.947 -4.172 1.00 94.49 15 A 1 ATOM 114 C CD1 . ILE A 1 15 ? -4.067 -2.637 -5.719 1.00 91.36 15 A 1 ATOM 115 N N . SER A 1 16 ? -2.729 -6.672 -4.352 1.00 95.60 16 A 1 ATOM 116 C CA . SER A 1 16 ? -1.701 -7.471 -5.018 1.00 93.67 16 A 1 ATOM 117 C C . SER A 1 16 ? -1.120 -8.506 -4.068 1.00 90.45 16 A 1 ATOM 118 O O . SER A 1 16 ? -0.105 -8.227 -3.411 1.00 85.49 16 A 1 ATOM 119 C CB . SER A 1 16 ? -0.594 -6.572 -5.548 1.00 90.35 16 A 1 ATOM 120 O OG . SER A 1 16 ? -1.095 -5.634 -6.466 1.00 82.01 16 A 1 ATOM 121 O OXT . SER A 1 16 ? -1.698 -9.602 -3.972 1.00 83.24 16 A 1 #