# 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_spkb32641 # _entry.id spkb32641 # 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" "C5 H10 N2 O3" 146.144 GLN y GLUTAMINE C(CC(=O)N)[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 H10 N3 O2" 156.162 HIS y HISTIDINE c1c([nH+]c[nH]1)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" "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" # _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 TYR 2 1 n HIS 3 1 n GLN 4 1 n LEU 5 1 n ILE 6 1 n LEU 7 1 n LEU 8 1 n ALA 9 1 n LEU 10 1 n ILE 11 1 n GLY 12 1 n THR 13 1 n ILE 14 1 n MET 15 1 n ALA 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 @ 2025-07-02 11:08:28)" _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 95.40 _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 89.62 1 1 A TYR 2 2 93.26 1 2 A HIS 3 2 93.22 1 3 A GLN 4 2 94.70 1 4 A LEU 5 2 96.44 1 5 A ILE 6 2 97.66 1 6 A LEU 7 2 97.28 1 7 A LEU 8 2 96.55 1 8 A ALA 9 2 98.43 1 9 A LEU 10 2 97.25 1 10 A ILE 11 2 97.45 1 11 A GLY 12 2 98.39 1 12 A THR 13 2 96.98 1 13 A ILE 14 2 96.68 1 14 A MET 15 2 93.14 1 15 A ALA 16 2 93.30 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 TYR . 2 A 2 A 3 1 n HIS . 3 A 3 A 4 1 n GLN . 4 A 4 A 5 1 n LEU . 5 A 5 A 6 1 n ILE . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n ALA . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n ILE . 11 A 11 A 12 1 n GLY . 12 A 12 A 13 1 n THR . 13 A 13 A 14 1 n ILE . 14 A 14 A 15 1 n MET . 15 A 15 A 16 1 n ALA . 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 ? -8.147 -6.995 0.306 1.00 91.61 1 A 1 ATOM 2 C CA . MET A 1 1 ? -7.076 -6.827 1.290 1.00 94.31 1 A 1 ATOM 3 C C . MET A 1 1 ? -5.982 -5.927 0.728 1.00 95.30 1 A 1 ATOM 4 O O . MET A 1 1 ? -4.843 -6.346 0.524 1.00 94.54 1 A 1 ATOM 5 C CB . MET A 1 1 ? -6.495 -8.188 1.676 1.00 90.91 1 A 1 ATOM 6 C CG . MET A 1 1 ? -5.651 -8.141 2.935 1.00 86.66 1 A 1 ATOM 7 S SD . MET A 1 1 ? -5.221 -9.791 3.504 1.00 85.76 1 A 1 ATOM 8 C CE . MET A 1 1 ? -4.346 -9.396 5.005 1.00 77.91 1 A 1 ATOM 9 N N . TYR A 1 2 ? -6.342 -4.700 0.468 1.00 95.30 2 A 1 ATOM 10 C CA . TYR A 1 2 ? -5.438 -3.730 -0.136 1.00 96.99 2 A 1 ATOM 11 C C . TYR A 1 2 ? -4.894 -2.750 0.903 1.00 97.90 2 A 1 ATOM 12 O O . TYR A 1 2 ? -4.394 -1.681 0.561 1.00 97.64 2 A 1 ATOM 13 C CB . TYR A 1 2 ? -6.161 -2.963 -1.246 1.00 96.24 2 A 1 ATOM 14 C CG . TYR A 1 2 ? -7.623 -3.333 -1.375 1.00 93.56 2 A 1 ATOM 15 C CD1 . TYR A 1 2 ? -8.556 -2.884 -0.453 1.00 92.01 2 A 1 ATOM 16 C CD2 . TYR A 1 2 ? -8.049 -4.137 -2.425 1.00 90.65 2 A 1 ATOM 17 C CE1 . TYR A 1 2 ? -9.893 -3.233 -0.573 1.00 90.56 2 A 1 ATOM 18 C CE2 . TYR A 1 2 ? -9.385 -4.484 -2.547 1.00 89.58 2 A 1 ATOM 19 C CZ . TYR A 1 2 ? -10.300 -4.029 -1.623 1.00 90.53 2 A 1 ATOM 20 O OH . TYR A 1 2 ? -11.625 -4.372 -1.737 1.00 88.14 2 A 1 ATOM 21 N N . HIS A 1 3 ? -5.015 -3.120 2.168 1.00 97.17 3 A 1 ATOM 22 C CA . HIS A 1 3 ? -4.563 -2.258 3.253 1.00 97.91 3 A 1 ATOM 23 C C . HIS A 1 3 ? -3.061 -2.009 3.167 1.00 98.43 3 A 1 ATOM 24 O O . HIS A 1 3 ? -2.594 -0.875 3.304 1.00 98.20 3 A 1 ATOM 25 C CB . HIS A 1 3 ? -4.904 -2.890 4.601 1.00 97.17 3 A 1 ATOM 26 C CG . HIS A 1 3 ? -6.305 -3.406 4.664 1.00 94.84 3 A 1 ATOM 27 N ND1 . HIS A 1 3 ? -6.660 -4.662 4.248 1.00 87.65 3 A 1 ATOM 28 C CD2 . HIS A 1 3 ? -7.434 -2.812 5.101 1.00 85.53 3 A 1 ATOM 29 C CE1 . HIS A 1 3 ? -7.961 -4.819 4.427 1.00 87.82 3 A 1 ATOM 30 N NE2 . HIS A 1 3 ? -8.460 -3.712 4.947 1.00 87.50 3 A 1 ATOM 31 N N . GLN A 1 4 ? -2.317 -3.077 2.928 1.00 97.75 4 A 1 ATOM 32 C CA . GLN A 1 4 ? -0.871 -2.956 2.810 1.00 98.23 4 A 1 ATOM 33 C C . GLN A 1 4 ? -0.493 -2.078 1.629 1.00 98.58 4 A 1 ATOM 34 O O . GLN A 1 4 ? 0.491 -1.340 1.683 1.00 98.36 4 A 1 ATOM 35 C CB . GLN A 1 4 ? -0.230 -4.332 2.648 1.00 97.89 4 A 1 ATOM 36 C CG . GLN A 1 4 ? -0.639 -5.072 1.410 1.00 95.12 4 A 1 ATOM 37 C CD . GLN A 1 4 ? 0.494 -5.872 0.813 1.00 92.71 4 A 1 ATOM 38 O OE1 . GLN A 1 4 ? 0.436 -6.264 -0.348 1.00 87.44 4 A 1 ATOM 39 N NE2 . GLN A 1 4 ? 1.548 -6.094 1.579 1.00 86.25 4 A 1 ATOM 40 N N . LEU A 1 5 ? -1.275 -2.157 0.567 1.00 97.87 5 A 1 ATOM 41 C CA . LEU A 1 5 ? -1.028 -1.353 -0.624 1.00 98.14 5 A 1 ATOM 42 C C . LEU A 1 5 ? -1.168 0.127 -0.302 1.00 98.45 5 A 1 ATOM 43 O O . LEU A 1 5 ? -0.339 0.946 -0.703 1.00 98.31 5 A 1 ATOM 44 C CB . LEU A 1 5 ? -2.009 -1.737 -1.731 1.00 97.89 5 A 1 ATOM 45 C CG . LEU A 1 5 ? -1.950 -3.199 -2.154 1.00 95.26 5 A 1 ATOM 46 C CD1 . LEU A 1 5 ? -2.998 -3.483 -3.214 1.00 93.25 5 A 1 ATOM 47 C CD2 . LEU A 1 5 ? -0.561 -3.541 -2.673 1.00 92.38 5 A 1 ATOM 48 N N . ILE A 1 6 ? -2.216 0.442 0.426 1.00 98.53 6 A 1 ATOM 49 C CA . ILE A 1 6 ? -2.465 1.819 0.830 1.00 98.55 6 A 1 ATOM 50 C C . ILE A 1 6 ? -1.364 2.301 1.763 1.00 98.64 6 A 1 ATOM 51 O O . ILE A 1 6 ? -0.860 3.423 1.625 1.00 98.54 6 A 1 ATOM 52 C CB . ILE A 1 6 ? -3.826 1.943 1.533 1.00 98.44 6 A 1 ATOM 53 C CG1 . ILE A 1 6 ? -4.946 1.490 0.597 1.00 97.35 6 A 1 ATOM 54 C CG2 . ILE A 1 6 ? -4.056 3.379 1.983 1.00 97.07 6 A 1 ATOM 55 C CD1 . ILE A 1 6 ? -6.287 1.374 1.280 1.00 94.14 6 A 1 ATOM 56 N N . LEU A 1 7 ? -0.997 1.437 2.702 1.00 98.63 7 A 1 ATOM 57 C CA . LEU A 1 7 ? 0.057 1.761 3.656 1.00 98.61 7 A 1 ATOM 58 C C . LEU A 1 7 ? 1.367 2.011 2.928 1.00 98.68 7 A 1 ATOM 59 O O . LEU A 1 7 ? 2.073 2.982 3.201 1.00 98.66 7 A 1 ATOM 60 C CB . LEU A 1 7 ? 0.233 0.622 4.667 1.00 98.47 7 A 1 ATOM 61 C CG . LEU A 1 7 ? -0.381 0.887 6.041 1.00 95.69 7 A 1 ATOM 62 C CD1 . LEU A 1 7 ? 0.279 2.096 6.681 1.00 94.68 7 A 1 ATOM 63 C CD2 . LEU A 1 7 ? -1.877 1.107 5.909 1.00 94.85 7 A 1 ATOM 64 N N . LEU A 1 8 ? 1.685 1.119 1.999 1.00 98.23 8 A 1 ATOM 65 C CA . LEU A 1 8 ? 2.917 1.239 1.227 1.00 98.15 8 A 1 ATOM 66 C C . LEU A 1 8 ? 2.946 2.555 0.468 1.00 98.32 8 A 1 ATOM 67 O O . LEU A 1 8 ? 3.969 3.243 0.432 1.00 98.09 8 A 1 ATOM 68 C CB . LEU A 1 8 ? 3.035 0.074 0.245 1.00 97.82 8 A 1 ATOM 69 C CG . LEU A 1 8 ? 4.289 0.096 -0.619 1.00 95.13 8 A 1 ATOM 70 C CD1 . LEU A 1 8 ? 5.531 0.031 0.246 1.00 93.52 8 A 1 ATOM 71 C CD2 . LEU A 1 8 ? 4.264 -1.046 -1.614 1.00 93.17 8 A 1 ATOM 72 N N . ALA A 1 9 ? 1.824 2.889 -0.140 1.00 98.50 9 A 1 ATOM 73 C CA . ALA A 1 9 ? 1.718 4.133 -0.888 1.00 98.48 9 A 1 ATOM 74 C C . ALA A 1 9 ? 1.933 5.327 0.031 1.00 98.57 9 A 1 ATOM 75 O O . ALA A 1 9 ? 2.632 6.279 -0.325 1.00 98.30 9 A 1 ATOM 76 C CB . ALA A 1 9 ? 0.354 4.226 -1.556 1.00 98.28 9 A 1 ATOM 77 N N . LEU A 1 10 ? 1.343 5.251 1.206 1.00 98.56 10 A 1 ATOM 78 C CA . LEU A 1 10 ? 1.479 6.314 2.192 1.00 98.53 10 A 1 ATOM 79 C C . LEU A 1 10 ? 2.930 6.459 2.627 1.00 98.63 10 A 1 ATOM 80 O O . LEU A 1 10 ? 3.451 7.572 2.724 1.00 98.40 10 A 1 ATOM 81 C CB . LEU A 1 10 ? 0.605 6.021 3.407 1.00 98.36 10 A 1 ATOM 82 C CG . LEU A 1 10 ? 0.611 7.112 4.474 1.00 96.18 10 A 1 ATOM 83 C CD1 . LEU A 1 10 ? 0.044 8.403 3.914 1.00 94.66 10 A 1 ATOM 84 C CD2 . LEU A 1 10 ? -0.180 6.665 5.690 1.00 94.65 10 A 1 ATOM 85 N N . ILE A 1 11 ? 3.569 5.326 2.884 1.00 98.53 11 A 1 ATOM 86 C CA . ILE A 1 11 ? 4.966 5.318 3.301 1.00 98.39 11 A 1 ATOM 87 C C . ILE A 1 11 ? 5.835 5.961 2.236 1.00 98.46 11 A 1 ATOM 88 O O . ILE A 1 11 ? 6.723 6.762 2.528 1.00 98.12 11 A 1 ATOM 89 C CB . ILE A 1 11 ? 5.452 3.886 3.571 1.00 98.07 11 A 1 ATOM 90 C CG1 . ILE A 1 11 ? 4.706 3.285 4.764 1.00 96.80 11 A 1 ATOM 91 C CG2 . ILE A 1 11 ? 6.953 3.877 3.828 1.00 96.87 11 A 1 ATOM 92 C CD1 . ILE A 1 11 ? 4.907 4.069 6.046 1.00 94.35 11 A 1 ATOM 93 N N . GLY A 1 12 ? 5.585 5.586 0.999 1.00 98.48 12 A 1 ATOM 94 C CA . GLY A 1 12 ? 6.340 6.147 -0.108 1.00 98.37 12 A 1 ATOM 95 C C . GLY A 1 12 ? 6.209 7.652 -0.165 1.00 98.52 12 A 1 ATOM 96 O O . GLY A 1 12 ? 7.185 8.367 -0.402 1.00 98.20 12 A 1 ATOM 97 N N . THR A 1 13 ? 5.001 8.128 0.060 1.00 98.50 13 A 1 ATOM 98 C CA . THR A 1 13 ? 4.735 9.563 0.053 1.00 98.44 13 A 1 ATOM 99 C C . THR A 1 13 ? 5.462 10.256 1.199 1.00 98.59 13 A 1 ATOM 100 O O . THR A 1 13 ? 6.032 11.335 1.024 1.00 97.98 13 A 1 ATOM 101 C CB . THR A 1 13 ? 3.236 9.847 0.179 1.00 97.79 13 A 1 ATOM 102 O OG1 . THR A 1 13 ? 2.535 9.166 -0.864 1.00 93.94 13 A 1 ATOM 103 C CG2 . THR A 1 13 ? 2.962 11.331 0.085 1.00 93.63 13 A 1 ATOM 104 N N . ILE A 1 14 ? 5.441 9.621 2.360 1.00 98.33 14 A 1 ATOM 105 C CA . ILE A 1 14 ? 6.102 10.170 3.536 1.00 98.23 14 A 1 ATOM 106 C C . ILE A 1 14 ? 7.610 10.216 3.335 1.00 98.31 14 A 1 ATOM 107 O O . ILE A 1 14 ? 8.273 11.186 3.706 1.00 97.74 14 A 1 ATOM 108 C CB . ILE A 1 14 ? 5.779 9.336 4.785 1.00 97.73 14 A 1 ATOM 109 C CG1 . ILE A 1 14 ? 4.281 9.397 5.077 1.00 95.66 14 A 1 ATOM 110 C CG2 . ILE A 1 14 ? 6.573 9.841 5.981 1.00 95.22 14 A 1 ATOM 111 C CD1 . ILE A 1 14 ? 3.845 8.423 6.143 1.00 92.21 14 A 1 ATOM 112 N N . MET A 1 15 ? 8.139 9.149 2.759 1.00 98.12 15 A 1 ATOM 113 C CA . MET A 1 15 ? 9.571 9.060 2.515 1.00 97.90 15 A 1 ATOM 114 C C . MET A 1 15 ? 10.019 10.119 1.522 1.00 98.03 15 A 1 ATOM 115 O O . MET A 1 15 ? 11.145 10.613 1.591 1.00 97.07 15 A 1 ATOM 116 C CB . MET A 1 15 ? 9.939 7.673 1.992 1.00 96.85 15 A 1 ATOM 117 C CG . MET A 1 15 ? 9.789 6.585 3.029 1.00 92.83 15 A 1 ATOM 118 S SD . MET A 1 15 ? 10.269 4.964 2.409 1.00 86.95 15 A 1 ATOM 119 C CE . MET A 1 15 ? 12.032 5.204 2.225 1.00 77.34 15 A 1 ATOM 120 N N . ALA A 1 16 ? 9.148 10.441 0.611 1.00 96.68 16 A 1 ATOM 121 C CA . ALA A 1 16 ? 9.436 11.439 -0.411 1.00 95.99 16 A 1 ATOM 122 C C . ALA A 1 16 ? 9.377 12.839 0.192 1.00 95.27 16 A 1 ATOM 123 O O . ALA A 1 16 ? 10.424 13.492 0.313 1.00 92.16 16 A 1 ATOM 124 C CB . ALA A 1 16 ? 8.463 11.307 -1.572 1.00 93.78 16 A 1 ATOM 125 O OXT . ALA A 1 16 ? 8.292 13.282 0.531 1.00 85.94 16 A 1 #