# 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_spkb32688 # _entry.id spkb32688 # 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 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" "C3 H7 N O3" 105.093 SER y SERINE C([C@@H](C(=O)O)N)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" "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 PHE 3 1 n SER 4 1 n LYS 5 1 n THR 6 1 n LEU 7 1 n LEU 8 1 n LEU 9 1 n ALA 10 1 n LEU 11 1 n VAL 12 1 n ALA 13 1 n GLY 14 1 n ALA 15 1 n LEU 16 1 n ALA 17 # _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 @ 2025-07-13 13:01:56)" _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 91.88 _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 78.89 1 1 A LYS 2 2 80.93 1 2 A PHE 3 2 85.55 1 3 A SER 4 2 94.28 1 4 A LYS 5 2 91.47 1 5 A THR 6 2 95.58 1 6 A LEU 7 2 94.39 1 7 A LEU 8 2 94.09 1 8 A LEU 9 2 94.93 1 9 A ALA 10 2 97.64 1 10 A LEU 11 2 95.06 1 11 A VAL 12 2 96.76 1 12 A ALA 13 2 97.71 1 13 A GLY 14 2 97.92 1 14 A ALA 15 2 97.64 1 15 A LEU 16 2 93.54 1 16 A ALA 17 2 90.20 1 17 # _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 SER . 4 A 4 A 5 1 n LYS . 5 A 5 A 6 1 n THR . 6 A 6 A 7 1 n LEU . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n LEU . 9 A 9 A 10 1 n ALA . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n VAL . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n GLY . 14 A 14 A 15 1 n ALA . 15 A 15 A 16 1 n LEU . 16 A 16 A 17 1 n ALA . 17 A 17 # _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 ? -8.153 8.871 12.130 1.00 82.32 1 A 1 ATOM 2 C CA . MET A 1 1 ? -8.739 7.850 11.253 1.00 85.30 1 A 1 ATOM 3 C C . MET A 1 1 ? -7.720 6.752 10.962 1.00 86.77 1 A 1 ATOM 4 O O . MET A 1 1 ? -6.524 6.916 11.224 1.00 82.52 1 A 1 ATOM 5 C CB . MET A 1 1 ? -9.216 8.459 9.933 1.00 79.21 1 A 1 ATOM 6 C CG . MET A 1 1 ? -8.104 9.119 9.137 1.00 77.29 1 A 1 ATOM 7 S SD . MET A 1 1 ? -8.722 9.906 7.641 1.00 73.35 1 A 1 ATOM 8 C CE . MET A 1 1 ? -7.213 10.574 6.981 1.00 64.35 1 A 1 ATOM 9 N N . LYS A 1 2 ? -8.180 5.638 10.400 1.00 84.24 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -7.299 4.517 10.076 1.00 87.88 2 A 1 ATOM 11 C C . LYS A 1 2 ? -6.611 4.739 8.739 1.00 90.01 2 A 1 ATOM 12 O O . LYS A 1 2 ? -7.145 5.396 7.849 1.00 88.31 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -8.102 3.217 10.035 1.00 84.01 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -8.722 2.832 11.368 1.00 78.41 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -7.673 2.554 12.428 1.00 78.15 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -6.854 1.318 12.076 1.00 71.67 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -7.697 0.100 12.006 1.00 65.73 2 A 1 ATOM 18 N N . PHE A 1 3 ? -5.414 4.170 8.600 1.00 88.24 3 A 1 ATOM 19 C CA . PHE A 1 3 ? -4.659 4.255 7.360 1.00 90.27 3 A 1 ATOM 20 C C . PHE A 1 3 ? -5.065 3.115 6.440 1.00 93.08 3 A 1 ATOM 21 O O . PHE A 1 3 ? -5.222 1.975 6.881 1.00 90.73 3 A 1 ATOM 22 C CB . PHE A 1 3 ? -3.158 4.172 7.635 1.00 88.65 3 A 1 ATOM 23 C CG . PHE A 1 3 ? -2.613 5.381 8.343 1.00 85.65 3 A 1 ATOM 24 C CD1 . PHE A 1 3 ? -2.263 6.512 7.628 1.00 82.43 3 A 1 ATOM 25 C CD2 . PHE A 1 3 ? -2.455 5.378 9.714 1.00 81.79 3 A 1 ATOM 26 C CE1 . PHE A 1 3 ? -1.756 7.631 8.269 1.00 80.66 3 A 1 ATOM 27 C CE2 . PHE A 1 3 ? -1.954 6.494 10.370 1.00 80.73 3 A 1 ATOM 28 C CZ . PHE A 1 3 ? -1.604 7.622 9.647 1.00 78.78 3 A 1 ATOM 29 N N . SER A 1 4 ? -5.225 3.425 5.166 1.00 95.50 4 A 1 ATOM 30 C CA . SER A 1 4 ? -5.593 2.410 4.191 1.00 96.21 4 A 1 ATOM 31 C C . SER A 1 4 ? -4.376 1.562 3.838 1.00 96.92 4 A 1 ATOM 32 O O . SER A 1 4 ? -3.301 2.094 3.560 1.00 96.30 4 A 1 ATOM 33 C CB . SER A 1 4 ? -6.151 3.049 2.923 1.00 95.14 4 A 1 ATOM 34 O OG . SER A 1 4 ? -6.466 2.061 1.961 1.00 85.63 4 A 1 ATOM 35 N N . LYS A 1 5 ? -4.565 0.236 3.850 1.00 95.47 5 A 1 ATOM 36 C CA . LYS A 1 5 ? -3.489 -0.684 3.514 1.00 96.42 5 A 1 ATOM 37 C C . LYS A 1 5 ? -2.990 -0.435 2.094 1.00 96.96 5 A 1 ATOM 38 O O . LYS A 1 5 ? -1.809 -0.612 1.804 1.00 96.61 5 A 1 ATOM 39 C CB . LYS A 1 5 ? -3.962 -2.134 3.658 1.00 95.97 5 A 1 ATOM 40 C CG . LYS A 1 5 ? -5.129 -2.476 2.752 1.00 92.29 5 A 1 ATOM 41 C CD . LYS A 1 5 ? -5.514 -3.936 2.853 1.00 88.46 5 A 1 ATOM 42 C CE . LYS A 1 5 ? -6.684 -4.255 1.931 1.00 83.78 5 A 1 ATOM 43 N NZ . LYS A 1 5 ? -6.363 -3.937 0.514 1.00 77.24 5 A 1 ATOM 44 N N . THR A 1 6 ? -3.896 -0.027 1.232 1.00 96.83 6 A 1 ATOM 45 C CA . THR A 1 6 ? -3.566 0.241 -0.165 1.00 96.93 6 A 1 ATOM 46 C C . THR A 1 6 ? -2.629 1.440 -0.284 1.00 97.30 6 A 1 ATOM 47 O O . THR A 1 6 ? -1.665 1.415 -1.052 1.00 96.58 6 A 1 ATOM 48 C CB . THR A 1 6 ? -4.831 0.506 -0.986 1.00 96.48 6 A 1 ATOM 49 O OG1 . THR A 1 6 ? -5.749 -0.568 -0.804 1.00 93.34 6 A 1 ATOM 50 C CG2 . THR A 1 6 ? -4.489 0.633 -2.461 1.00 91.60 6 A 1 ATOM 51 N N . LEU A 1 7 ? -2.907 2.472 0.498 1.00 96.89 7 A 1 ATOM 52 C CA . LEU A 1 7 ? -2.076 3.669 0.490 1.00 96.84 7 A 1 ATOM 53 C C . LEU A 1 7 ? -0.671 3.356 0.985 1.00 97.33 7 A 1 ATOM 54 O O . LEU A 1 7 ? 0.319 3.797 0.395 1.00 97.11 7 A 1 ATOM 55 C CB . LEU A 1 7 ? -2.702 4.754 1.368 1.00 96.65 7 A 1 ATOM 56 C CG . LEU A 1 7 ? -4.007 5.332 0.831 1.00 91.36 7 A 1 ATOM 57 C CD1 . LEU A 1 7 ? -4.610 6.290 1.842 1.00 89.00 7 A 1 ATOM 58 C CD2 . LEU A 1 7 ? -3.774 6.038 -0.495 1.00 89.97 7 A 1 ATOM 59 N N . LEU A 1 8 ? -0.594 2.593 2.070 1.00 96.16 8 A 1 ATOM 60 C CA . LEU A 1 8 ? 0.696 2.209 2.637 1.00 96.55 8 A 1 ATOM 61 C C . LEU A 1 8 ? 1.463 1.311 1.675 1.00 97.28 8 A 1 ATOM 62 O O . LEU A 1 8 ? 2.669 1.478 1.482 1.00 97.52 8 A 1 ATOM 63 C CB . LEU A 1 8 ? 0.491 1.493 3.970 1.00 96.52 8 A 1 ATOM 64 C CG . LEU A 1 8 ? 1.785 1.170 4.710 1.00 89.80 8 A 1 ATOM 65 C CD1 . LEU A 1 8 ? 2.526 2.439 5.090 1.00 88.86 8 A 1 ATOM 66 C CD2 . LEU A 1 8 ? 1.493 0.336 5.949 1.00 90.04 8 A 1 ATOM 67 N N . LEU A 1 9 ? 0.765 0.356 1.080 1.00 97.27 9 A 1 ATOM 68 C CA . LEU A 1 9 ? 1.375 -0.572 0.132 1.00 97.40 9 A 1 ATOM 69 C C . LEU A 1 9 ? 1.917 0.173 -1.082 1.00 97.86 9 A 1 ATOM 70 O O . LEU A 1 9 ? 3.011 -0.126 -1.568 1.00 97.84 9 A 1 ATOM 71 C CB . LEU A 1 9 ? 0.348 -1.612 -0.313 1.00 96.97 9 A 1 ATOM 72 C CG . LEU A 1 9 ? 0.901 -2.693 -1.237 1.00 91.49 9 A 1 ATOM 73 C CD1 . LEU A 1 9 ? 1.953 -3.519 -0.527 1.00 90.04 9 A 1 ATOM 74 C CD2 . LEU A 1 9 ? -0.223 -3.575 -1.750 1.00 90.59 9 A 1 ATOM 75 N N . ALA A 1 10 ? 1.155 1.134 -1.560 1.00 97.56 10 A 1 ATOM 76 C CA . ALA A 1 10 ? 1.563 1.931 -2.711 1.00 97.69 10 A 1 ATOM 77 C C . ALA A 1 10 ? 2.828 2.729 -2.402 1.00 98.11 10 A 1 ATOM 78 O O . ALA A 1 10 ? 3.722 2.844 -3.242 1.00 97.64 10 A 1 ATOM 79 C CB . ALA A 1 10 ? 0.436 2.873 -3.119 1.00 97.22 10 A 1 ATOM 80 N N . LEU A 1 11 ? 2.895 3.263 -1.188 1.00 97.38 11 A 1 ATOM 81 C CA . LEU A 1 11 ? 4.056 4.036 -0.761 1.00 97.47 11 A 1 ATOM 82 C C . LEU A 1 11 ? 5.296 3.156 -0.693 1.00 97.97 11 A 1 ATOM 83 O O . LEU A 1 11 ? 6.371 3.541 -1.160 1.00 97.66 11 A 1 ATOM 84 C CB . LEU A 1 11 ? 3.789 4.669 0.605 1.00 97.01 11 A 1 ATOM 85 C CG . LEU A 1 11 ? 4.910 5.573 1.115 1.00 92.56 11 A 1 ATOM 86 C CD1 . LEU A 1 11 ? 5.081 6.778 0.207 1.00 89.79 11 A 1 ATOM 87 C CD2 . LEU A 1 11 ? 4.624 6.019 2.540 1.00 90.66 11 A 1 ATOM 88 N N . VAL A 1 12 ? 5.142 1.972 -0.106 1.00 97.48 12 A 1 ATOM 89 C CA . VAL A 1 12 ? 6.246 1.023 0.014 1.00 97.61 12 A 1 ATOM 90 C C . VAL A 1 12 ? 6.709 0.562 -1.362 1.00 97.98 12 A 1 ATOM 91 O O . VAL A 1 12 ? 7.912 0.473 -1.629 1.00 97.69 12 A 1 ATOM 92 C CB . VAL A 1 12 ? 5.837 -0.192 0.864 1.00 97.02 12 A 1 ATOM 93 C CG1 . VAL A 1 12 ? 6.941 -1.239 0.880 1.00 94.59 12 A 1 ATOM 94 C CG2 . VAL A 1 12 ? 5.513 0.245 2.282 1.00 94.97 12 A 1 ATOM 95 N N . ALA A 1 13 ? 5.758 0.275 -2.232 1.00 97.88 13 A 1 ATOM 96 C CA . ALA A 1 13 ? 6.072 -0.172 -3.585 1.00 97.87 13 A 1 ATOM 97 C C . ALA A 1 13 ? 6.873 0.887 -4.338 1.00 98.11 13 A 1 ATOM 98 O O . ALA A 1 13 ? 7.829 0.571 -5.046 1.00 97.46 13 A 1 ATOM 99 C CB . ALA A 1 13 ? 4.788 -0.496 -4.341 1.00 97.23 13 A 1 ATOM 100 N N . GLY A 1 14 ? 6.490 2.134 -4.171 1.00 97.98 14 A 1 ATOM 101 C CA . GLY A 1 14 ? 7.199 3.229 -4.816 1.00 97.86 14 A 1 ATOM 102 C C . GLY A 1 14 ? 8.596 3.415 -4.254 1.00 98.13 14 A 1 ATOM 103 O O . GLY A 1 14 ? 9.524 3.774 -4.978 1.00 97.72 14 A 1 ATOM 104 N N . ALA A 1 15 ? 8.752 3.167 -2.958 1.00 98.00 15 A 1 ATOM 105 C CA . ALA A 1 15 ? 10.042 3.306 -2.295 1.00 97.89 15 A 1 ATOM 106 C C . ALA A 1 15 ? 11.033 2.241 -2.750 1.00 98.10 15 A 1 ATOM 107 O O . ALA A 1 15 ? 12.208 2.536 -2.973 1.00 97.02 15 A 1 ATOM 108 C CB . ALA A 1 15 ? 9.862 3.238 -0.781 1.00 97.18 15 A 1 ATOM 109 N N . LEU A 1 16 ? 10.576 0.996 -2.867 1.00 97.39 16 A 1 ATOM 110 C CA . LEU A 1 16 ? 11.440 -0.104 -3.280 1.00 96.99 16 A 1 ATOM 111 C C . LEU A 1 16 ? 11.633 -0.144 -4.789 1.00 97.11 16 A 1 ATOM 112 O O . LEU A 1 16 ? 12.573 -0.775 -5.287 1.00 95.46 16 A 1 ATOM 113 C CB . LEU A 1 16 ? 10.879 -1.435 -2.769 1.00 95.62 16 A 1 ATOM 114 C CG . LEU A 1 16 ? 9.516 -1.839 -3.333 1.00 91.37 16 A 1 ATOM 115 C CD1 . LEU A 1 16 ? 9.662 -2.596 -4.639 1.00 87.79 16 A 1 ATOM 116 C CD2 . LEU A 1 16 ? 8.764 -2.693 -2.323 1.00 86.56 16 A 1 ATOM 117 N N . ALA A 1 17 ? 10.764 0.513 -5.524 1.00 95.33 17 A 1 ATOM 118 C CA . ALA A 1 17 ? 10.839 0.539 -6.972 1.00 93.94 17 A 1 ATOM 119 C C . ALA A 1 17 ? 11.975 1.450 -7.440 1.00 92.86 17 A 1 ATOM 120 O O . ALA A 1 17 ? 12.183 2.511 -6.835 1.00 87.29 17 A 1 ATOM 121 C CB . ALA A 1 17 ? 9.510 0.981 -7.572 1.00 90.12 17 A 1 ATOM 122 O OXT . ALA A 1 17 ? 12.658 1.105 -8.407 1.00 81.68 17 A 1 #