# 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_spkb25257 # _entry.id spkb25257 # 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" "C9 H11 N O2" 165.189 PHE y PHENYLALANINE c1ccc(cc1)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 PHE 3 1 n PHE 4 1 n ALA 5 1 n ILE 6 1 n ALA 7 1 n ALA 8 1 n LEU 9 1 n PHE 10 1 n ALA 11 1 n GLY 12 1 n ALA 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 @ 2025-07-07 04:44:15)" _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 91.60 _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 85.60 1 1 A LYS 2 2 88.54 1 2 A PHE 3 2 87.30 1 3 A PHE 4 2 88.12 1 4 A ALA 5 2 95.10 1 5 A ILE 6 2 94.15 1 6 A ALA 7 2 96.92 1 7 A ALA 8 2 96.23 1 8 A LEU 9 2 94.33 1 9 A PHE 10 2 92.36 1 10 A ALA 11 2 96.59 1 11 A GLY 12 2 96.12 1 12 A ALA 13 2 96.40 1 13 A LEU 14 2 91.50 1 14 A ALA 15 2 87.67 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 PHE . 3 A 3 A 4 1 n PHE . 4 A 4 A 5 1 n ALA . 5 A 5 A 6 1 n ILE . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n PHE . 10 A 10 A 11 1 n ALA . 11 A 11 A 12 1 n GLY . 12 A 12 A 13 1 n ALA . 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 ? -9.681 7.233 5.421 1.00 88.17 1 A 1 ATOM 2 C CA . MET A 1 1 ? -8.915 6.497 4.398 1.00 90.93 1 A 1 ATOM 3 C C . MET A 1 1 ? -8.239 5.259 4.993 1.00 92.46 1 A 1 ATOM 4 O O . MET A 1 1 ? -7.076 5.301 5.384 1.00 89.82 1 A 1 ATOM 5 C CB . MET A 1 1 ? -7.862 7.409 3.769 1.00 86.57 1 A 1 ATOM 6 C CG . MET A 1 1 ? -7.118 8.271 4.781 1.00 83.78 1 A 1 ATOM 7 S SD . MET A 1 1 ? -6.203 9.587 3.968 1.00 81.45 1 A 1 ATOM 8 C CE . MET A 1 1 ? -6.410 10.899 5.154 1.00 71.65 1 A 1 ATOM 9 N N . LYS A 1 2 ? -8.997 4.169 5.061 1.00 92.68 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -8.481 2.915 5.609 1.00 93.72 2 A 1 ATOM 11 C C . LYS A 1 2 ? -7.815 2.081 4.520 1.00 94.48 2 A 1 ATOM 12 O O . LYS A 1 2 ? -6.725 1.546 4.709 1.00 94.26 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -9.632 2.142 6.255 1.00 92.37 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -9.172 0.912 7.006 1.00 88.48 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -8.783 1.249 8.438 1.00 85.49 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -8.335 0.003 9.166 1.00 80.76 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -7.937 0.317 10.563 1.00 74.59 2 A 1 ATOM 18 N N . PHE A 1 3 ? -8.482 1.973 3.379 1.00 88.30 3 A 1 ATOM 19 C CA . PHE A 1 3 ? -7.963 1.204 2.248 1.00 90.55 3 A 1 ATOM 20 C C . PHE A 1 3 ? -6.732 1.867 1.639 1.00 94.00 3 A 1 ATOM 21 O O . PHE A 1 3 ? -5.942 1.216 0.954 1.00 92.76 3 A 1 ATOM 22 C CB . PHE A 1 3 ? -9.049 1.052 1.187 1.00 89.13 3 A 1 ATOM 23 C CG . PHE A 1 3 ? -9.973 -0.103 1.462 1.00 87.79 3 A 1 ATOM 24 C CD1 . PHE A 1 3 ? -10.917 -0.030 2.466 1.00 85.17 3 A 1 ATOM 25 C CD2 . PHE A 1 3 ? -9.882 -1.260 0.702 1.00 85.11 3 A 1 ATOM 26 C CE1 . PHE A 1 3 ? -11.762 -1.096 2.724 1.00 83.16 3 A 1 ATOM 27 C CE2 . PHE A 1 3 ? -10.725 -2.327 0.950 1.00 82.43 3 A 1 ATOM 28 C CZ . PHE A 1 3 ? -11.667 -2.248 1.963 1.00 81.94 3 A 1 ATOM 29 N N . PHE A 1 4 ? -6.568 3.144 1.899 1.00 89.61 4 A 1 ATOM 30 C CA . PHE A 1 4 ? -5.420 3.886 1.388 1.00 90.88 4 A 1 ATOM 31 C C . PHE A 1 4 ? -4.117 3.316 1.938 1.00 93.73 4 A 1 ATOM 32 O O . PHE A 1 4 ? -3.115 3.232 1.227 1.00 92.96 4 A 1 ATOM 33 C CB . PHE A 1 4 ? -5.539 5.360 1.771 1.00 90.27 4 A 1 ATOM 34 C CG . PHE A 1 4 ? -5.942 6.234 0.615 1.00 87.93 4 A 1 ATOM 35 C CD1 . PHE A 1 4 ? -5.049 6.477 -0.416 1.00 84.37 4 A 1 ATOM 36 C CD2 . PHE A 1 4 ? -7.201 6.816 0.570 1.00 85.46 4 A 1 ATOM 37 C CE1 . PHE A 1 4 ? -5.411 7.286 -1.485 1.00 84.24 4 A 1 ATOM 38 C CE2 . PHE A 1 4 ? -7.565 7.627 -0.494 1.00 85.01 4 A 1 ATOM 39 C CZ . PHE A 1 4 ? -6.670 7.862 -1.527 1.00 84.90 4 A 1 ATOM 40 N N . ALA A 1 5 ? -4.140 2.910 3.212 1.00 94.20 5 A 1 ATOM 41 C CA . ALA A 1 5 ? -2.961 2.344 3.861 1.00 95.15 5 A 1 ATOM 42 C C . ALA A 1 5 ? -2.570 1.012 3.231 1.00 96.22 5 A 1 ATOM 43 O O . ALA A 1 5 ? -1.390 0.740 3.010 1.00 95.45 5 A 1 ATOM 44 C CB . ALA A 1 5 ? -3.228 2.165 5.350 1.00 94.48 5 A 1 ATOM 45 N N . ILE A 1 6 ? -3.568 0.189 2.954 1.00 96.09 6 A 1 ATOM 46 C CA . ILE A 1 6 ? -3.339 -1.121 2.348 1.00 96.12 6 A 1 ATOM 47 C C . ILE A 1 6 ? -2.799 -0.973 0.929 1.00 96.71 6 A 1 ATOM 48 O O . ILE A 1 6 ? -1.859 -1.663 0.531 1.00 96.66 6 A 1 ATOM 49 C CB . ILE A 1 6 ? -4.634 -1.949 2.339 1.00 95.93 6 A 1 ATOM 50 C CG1 . ILE A 1 6 ? -5.177 -2.108 3.761 1.00 92.98 6 A 1 ATOM 51 C CG2 . ILE A 1 6 ? -4.373 -3.323 1.722 1.00 92.56 6 A 1 ATOM 52 C CD1 . ILE A 1 6 ? -6.605 -2.601 3.790 1.00 86.11 6 A 1 ATOM 53 N N . ALA A 1 7 ? -3.404 -0.081 0.183 1.00 96.98 7 A 1 ATOM 54 C CA . ALA A 1 7 ? -2.990 0.155 -1.196 1.00 96.90 7 A 1 ATOM 55 C C . ALA A 1 7 ? -1.571 0.712 -1.255 1.00 97.26 7 A 1 ATOM 56 O O . ALA A 1 7 ? -0.772 0.314 -2.100 1.00 96.99 7 A 1 ATOM 57 C CB . ALA A 1 7 ? -3.959 1.119 -1.871 1.00 96.48 7 A 1 ATOM 58 N N . ALA A 1 8 ? -1.268 1.621 -0.348 1.00 96.50 8 A 1 ATOM 59 C CA . ALA A 1 8 ? 0.054 2.236 -0.293 1.00 96.14 8 A 1 ATOM 60 C C . ALA A 1 8 ? 1.113 1.221 0.123 1.00 96.91 8 A 1 ATOM 61 O O . ALA A 1 8 ? 2.215 1.206 -0.420 1.00 96.17 8 A 1 ATOM 62 C CB . ALA A 1 8 ? 0.043 3.405 0.681 1.00 95.45 8 A 1 ATOM 63 N N . LEU A 1 9 ? 0.766 0.378 1.093 1.00 95.51 9 A 1 ATOM 64 C CA . LEU A 1 9 ? 1.684 -0.651 1.582 1.00 95.74 9 A 1 ATOM 65 C C . LEU A 1 9 ? 1.976 -1.677 0.494 1.00 96.79 9 A 1 ATOM 66 O O . LEU A 1 9 ? 3.113 -2.122 0.337 1.00 96.44 9 A 1 ATOM 67 C CB . LEU A 1 9 ? 1.086 -1.346 2.807 1.00 95.41 9 A 1 ATOM 68 C CG . LEU A 1 9 ? 2.133 -1.927 3.753 1.00 92.89 9 A 1 ATOM 69 C CD1 . LEU A 1 9 ? 2.723 -0.835 4.631 1.00 90.88 9 A 1 ATOM 70 C CD2 . LEU A 1 9 ? 1.537 -3.025 4.608 1.00 90.97 9 A 1 ATOM 71 N N . PHE A 1 10 ? 0.948 -2.056 -0.233 1.00 95.47 10 A 1 ATOM 72 C CA . PHE A 1 10 ? 1.085 -3.032 -1.312 1.00 95.12 10 A 1 ATOM 73 C C . PHE A 1 10 ? 2.025 -2.511 -2.392 1.00 96.21 10 A 1 ATOM 74 O O . PHE A 1 10 ? 2.876 -3.245 -2.897 1.00 96.12 10 A 1 ATOM 75 C CB . PHE A 1 10 ? -0.285 -3.333 -1.913 1.00 94.59 10 A 1 ATOM 76 C CG . PHE A 1 10 ? -0.320 -4.639 -2.660 1.00 91.83 10 A 1 ATOM 77 C CD1 . PHE A 1 10 ? -0.354 -5.839 -1.972 1.00 89.30 10 A 1 ATOM 78 C CD2 . PHE A 1 10 ? -0.325 -4.658 -4.047 1.00 90.30 10 A 1 ATOM 79 C CE1 . PHE A 1 10 ? -0.388 -7.046 -2.655 1.00 89.21 10 A 1 ATOM 80 C CE2 . PHE A 1 10 ? -0.357 -5.864 -4.739 1.00 88.92 10 A 1 ATOM 81 C CZ . PHE A 1 10 ? -0.388 -7.061 -4.040 1.00 88.90 10 A 1 ATOM 82 N N . ALA A 1 11 ? 1.863 -1.266 -2.736 1.00 96.95 11 A 1 ATOM 83 C CA . ALA A 1 11 ? 2.702 -0.645 -3.756 1.00 96.73 11 A 1 ATOM 84 C C . ALA A 1 11 ? 4.134 -0.479 -3.261 1.00 97.09 11 A 1 ATOM 85 O O . ALA A 1 11 ? 5.087 -0.670 -4.014 1.00 96.13 11 A 1 ATOM 86 C CB . ALA A 1 11 ? 2.123 0.705 -4.151 1.00 96.06 11 A 1 ATOM 87 N N . GLY A 1 12 ? 4.276 -0.126 -1.989 1.00 96.31 12 A 1 ATOM 88 C CA . GLY A 1 12 ? 5.594 0.054 -1.393 1.00 95.64 12 A 1 ATOM 89 C C . GLY A 1 12 ? 6.327 -1.255 -1.202 1.00 96.58 12 A 1 ATOM 90 O O . GLY A 1 12 ? 7.534 -1.340 -1.423 1.00 95.96 12 A 1 ATOM 91 N N . ALA A 1 13 ? 5.593 -2.287 -0.783 1.00 96.59 13 A 1 ATOM 92 C CA . ALA A 1 13 ? 6.172 -3.613 -0.564 1.00 96.62 13 A 1 ATOM 93 C C . ALA A 1 13 ? 6.612 -4.243 -1.880 1.00 97.20 13 A 1 ATOM 94 O O . ALA A 1 13 ? 7.636 -4.924 -1.936 1.00 95.92 13 A 1 ATOM 95 C CB . ALA A 1 13 ? 5.159 -4.514 0.137 1.00 95.68 13 A 1 ATOM 96 N N . LEU A 1 14 ? 5.835 -4.027 -2.919 1.00 95.32 14 A 1 ATOM 97 C CA . LEU A 1 14 ? 6.150 -4.566 -4.243 1.00 94.61 14 A 1 ATOM 98 C C . LEU A 1 14 ? 7.390 -3.911 -4.821 1.00 94.64 14 A 1 ATOM 99 O O . LEU A 1 14 ? 8.158 -4.539 -5.554 1.00 92.99 14 A 1 ATOM 100 C CB . LEU A 1 14 ? 4.973 -4.357 -5.195 1.00 93.06 14 A 1 ATOM 101 C CG . LEU A 1 14 ? 4.939 -5.348 -6.345 1.00 90.23 14 A 1 ATOM 102 C CD1 . LEU A 1 14 ? 3.840 -6.367 -6.142 1.00 86.69 14 A 1 ATOM 103 C CD2 . LEU A 1 14 ? 4.755 -4.620 -7.668 1.00 84.50 14 A 1 ATOM 104 N N . ALA A 1 15 ? 7.588 -2.653 -4.498 1.00 93.31 15 A 1 ATOM 105 C CA . ALA A 1 15 ? 8.727 -1.894 -4.993 1.00 91.39 15 A 1 ATOM 106 C C . ALA A 1 15 ? 10.036 -2.418 -4.405 1.00 90.32 15 A 1 ATOM 107 O O . ALA A 1 15 ? 10.032 -2.907 -3.260 1.00 85.42 15 A 1 ATOM 108 C CB . ALA A 1 15 ? 8.550 -0.416 -4.685 1.00 86.46 15 A 1 ATOM 109 O OXT . ALA A 1 15 ? 11.071 -2.334 -5.075 1.00 79.13 15 A 1 #