# 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_spkb34062 # _entry.id spkb34062 # 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" "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 THR 3 1 n LEU 4 1 n PHE 5 1 n LEU 6 1 n ALA 7 1 n ILE 8 1 n ALA 9 1 n LEU 10 1 n PHE 11 1 n SER 12 1 n ALA 13 1 n VAL 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 @ 2025-07-12 22:15:18)" _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 92.85 _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 84.80 1 1 A LYS 2 2 88.65 1 2 A THR 3 2 90.42 1 3 A LEU 4 2 92.68 1 4 A PHE 5 2 91.64 1 5 A LEU 6 2 93.44 1 6 A ALA 7 2 97.14 1 7 A ILE 8 2 95.06 1 8 A ALA 9 2 96.93 1 9 A LEU 10 2 94.73 1 10 A PHE 11 2 92.73 1 11 A SER 12 2 95.74 1 12 A ALA 13 2 97.11 1 13 A VAL 14 2 96.47 1 14 A ALA 15 2 97.15 1 15 A LEU 16 2 92.11 1 16 A ALA 17 2 88.95 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 THR . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n PHE . 5 A 5 A 6 1 n LEU . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n ILE . 8 A 8 A 9 1 n ALA . 9 A 9 A 10 1 n LEU . 10 A 10 A 11 1 n PHE . 11 A 11 A 12 1 n SER . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n VAL . 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 ? -4.638 13.517 7.513 1.00 89.50 1 A 1 ATOM 2 C CA . MET A 1 1 ? -4.896 12.073 7.619 1.00 91.28 1 A 1 ATOM 3 C C . MET A 1 1 ? -4.359 11.352 6.381 1.00 91.96 1 A 1 ATOM 4 O O . MET A 1 1 ? -4.781 11.644 5.268 1.00 89.53 1 A 1 ATOM 5 C CB . MET A 1 1 ? -6.386 11.807 7.737 1.00 85.26 1 A 1 ATOM 6 C CG . MET A 1 1 ? -7.114 12.813 8.629 1.00 81.78 1 A 1 ATOM 7 S SD . MET A 1 1 ? -6.442 12.887 10.275 1.00 78.95 1 A 1 ATOM 8 C CE . MET A 1 1 ? -7.661 13.910 11.079 1.00 70.15 1 A 1 ATOM 9 N N . LYS A 1 2 ? -3.442 10.421 6.571 1.00 93.11 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -2.857 9.667 5.466 1.00 94.35 2 A 1 ATOM 11 C C . LYS A 1 2 ? -2.888 8.170 5.769 1.00 95.07 2 A 1 ATOM 12 O O . LYS A 1 2 ? -1.867 7.486 5.714 1.00 94.33 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -1.434 10.149 5.213 1.00 93.06 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -1.351 11.033 3.983 1.00 88.01 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 0.037 11.573 3.776 1.00 85.05 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 0.129 12.312 2.459 1.00 80.43 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 1.298 13.239 2.452 1.00 74.45 2 A 1 ATOM 18 N N . THR A 1 3 ? -4.069 7.687 6.092 1.00 91.43 3 A 1 ATOM 19 C CA . THR A 1 3 ? -4.249 6.272 6.411 1.00 92.72 3 A 1 ATOM 20 C C . THR A 1 3 ? -4.238 5.425 5.144 1.00 94.24 3 A 1 ATOM 21 O O . THR A 1 3 ? -3.840 4.261 5.167 1.00 92.48 3 A 1 ATOM 22 C CB . THR A 1 3 ? -5.569 6.059 7.158 1.00 91.07 3 A 1 ATOM 23 O OG1 . THR A 1 3 ? -5.717 7.052 8.164 1.00 86.42 3 A 1 ATOM 24 C CG2 . THR A 1 3 ? -5.611 4.687 7.802 1.00 84.59 3 A 1 ATOM 25 N N . LEU A 1 4 ? -4.668 6.019 4.042 1.00 94.10 4 A 1 ATOM 26 C CA . LEU A 1 4 ? -4.716 5.316 2.763 1.00 94.91 4 A 1 ATOM 27 C C . LEU A 1 4 ? -3.312 4.947 2.295 1.00 96.28 4 A 1 ATOM 28 O O . LEU A 1 4 ? -3.090 3.853 1.773 1.00 96.07 4 A 1 ATOM 29 C CB . LEU A 1 4 ? -5.405 6.193 1.718 1.00 94.71 4 A 1 ATOM 30 C CG . LEU A 1 4 ? -6.881 6.461 1.989 1.00 91.00 4 A 1 ATOM 31 C CD1 . LEU A 1 4 ? -7.381 7.599 1.114 1.00 87.11 4 A 1 ATOM 32 C CD2 . LEU A 1 4 ? -7.704 5.206 1.734 1.00 87.23 4 A 1 ATOM 33 N N . PHE A 1 5 ? -2.370 5.858 2.488 1.00 92.54 5 A 1 ATOM 34 C CA . PHE A 1 5 ? -0.987 5.623 2.095 1.00 93.62 5 A 1 ATOM 35 C C . PHE A 1 5 ? -0.401 4.440 2.850 1.00 95.14 5 A 1 ATOM 36 O O . PHE A 1 5 ? 0.306 3.611 2.278 1.00 94.92 5 A 1 ATOM 37 C CB . PHE A 1 5 ? -0.156 6.875 2.361 1.00 93.60 5 A 1 ATOM 38 C CG . PHE A 1 5 ? 0.498 7.403 1.112 1.00 91.97 5 A 1 ATOM 39 C CD1 . PHE A 1 5 ? -0.213 8.184 0.220 1.00 88.87 5 A 1 ATOM 40 C CD2 . PHE A 1 5 ? 1.822 7.103 0.841 1.00 90.03 5 A 1 ATOM 41 C CE1 . PHE A 1 5 ? 0.388 8.665 -0.932 1.00 88.96 5 A 1 ATOM 42 C CE2 . PHE A 1 5 ? 2.428 7.582 -0.311 1.00 88.87 5 A 1 ATOM 43 C CZ . PHE A 1 5 ? 1.712 8.366 -1.199 1.00 89.55 5 A 1 ATOM 44 N N . LEU A 1 6 ? -0.708 4.372 4.135 1.00 96.53 6 A 1 ATOM 45 C CA . LEU A 1 6 ? -0.219 3.281 4.975 1.00 96.33 6 A 1 ATOM 46 C C . LEU A 1 6 ? -0.826 1.956 4.534 1.00 97.09 6 A 1 ATOM 47 O O . LEU A 1 6 ? -0.147 0.926 4.512 1.00 97.19 6 A 1 ATOM 48 C CB . LEU A 1 6 ? -0.566 3.567 6.436 1.00 95.94 6 A 1 ATOM 49 C CG . LEU A 1 6 ? 0.652 3.685 7.343 1.00 89.10 6 A 1 ATOM 50 C CD1 . LEU A 1 6 ? 0.311 4.477 8.599 1.00 87.36 6 A 1 ATOM 51 C CD2 . LEU A 1 6 ? 1.174 2.312 7.714 1.00 88.00 6 A 1 ATOM 52 N N . ALA A 1 7 ? -2.101 1.993 4.178 1.00 96.82 7 A 1 ATOM 53 C CA . ALA A 1 7 ? -2.804 0.795 3.729 1.00 97.11 7 A 1 ATOM 54 C C . ALA A 1 7 ? -2.216 0.276 2.422 1.00 97.63 7 A 1 ATOM 55 O O . ALA A 1 7 ? -2.053 -0.933 2.242 1.00 97.31 7 A 1 ATOM 56 C CB . ALA A 1 7 ? -4.285 1.106 3.559 1.00 96.81 7 A 1 ATOM 57 N N . ILE A 1 8 ? -1.894 1.189 1.520 1.00 96.71 8 A 1 ATOM 58 C CA . ILE A 1 8 ? -1.319 0.821 0.231 1.00 96.30 8 A 1 ATOM 59 C C . ILE A 1 8 ? 0.056 0.199 0.423 1.00 96.55 8 A 1 ATOM 60 O O . ILE A 1 8 ? 0.412 -0.779 -0.242 1.00 96.62 8 A 1 ATOM 61 C CB . ILE A 1 8 ? -1.223 2.052 -0.687 1.00 96.49 8 A 1 ATOM 62 C CG1 . ILE A 1 8 ? -2.622 2.561 -1.043 1.00 94.38 8 A 1 ATOM 63 C CG2 . ILE A 1 8 ? -0.472 1.689 -1.975 1.00 93.73 8 A 1 ATOM 64 C CD1 . ILE A 1 8 ? -2.616 3.969 -1.596 1.00 89.69 8 A 1 ATOM 65 N N . ALA A 1 9 ? 0.828 0.776 1.328 1.00 97.11 9 A 1 ATOM 66 C CA . ALA A 1 9 ? 2.166 0.268 1.612 1.00 97.01 9 A 1 ATOM 67 C C . ALA A 1 9 ? 2.096 -1.153 2.162 1.00 97.39 9 A 1 ATOM 68 O O . ALA A 1 9 ? 2.886 -2.016 1.782 1.00 96.67 9 A 1 ATOM 69 C CB . ALA A 1 9 ? 2.865 1.185 2.609 1.00 96.46 9 A 1 ATOM 70 N N . LEU A 1 10 ? 1.144 -1.381 3.048 1.00 97.38 10 A 1 ATOM 71 C CA . LEU A 1 10 ? 0.957 -2.697 3.645 1.00 97.14 10 A 1 ATOM 72 C C . LEU A 1 10 ? 0.462 -3.693 2.606 1.00 97.36 10 A 1 ATOM 73 O O . LEU A 1 10 ? 0.905 -4.845 2.572 1.00 96.77 10 A 1 ATOM 74 C CB . LEU A 1 10 ? -0.043 -2.608 4.801 1.00 96.76 10 A 1 ATOM 75 C CG . LEU A 1 10 ? 0.003 -3.807 5.744 1.00 92.71 10 A 1 ATOM 76 C CD1 . LEU A 1 10 ? 1.244 -3.739 6.622 1.00 89.65 10 A 1 ATOM 77 C CD2 . LEU A 1 10 ? -1.244 -3.859 6.608 1.00 90.09 10 A 1 ATOM 78 N N . PHE A 1 11 ? -0.452 -3.244 1.762 1.00 95.41 11 A 1 ATOM 79 C CA . PHE A 1 11 ? -1.004 -4.081 0.703 1.00 95.19 11 A 1 ATOM 80 C C . PHE A 1 11 ? 0.086 -4.501 -0.273 1.00 96.23 11 A 1 ATOM 81 O O . PHE A 1 11 ? 0.090 -5.630 -0.770 1.00 95.59 11 A 1 ATOM 82 C CB . PHE A 1 11 ? -2.100 -3.315 -0.032 1.00 94.70 11 A 1 ATOM 83 C CG . PHE A 1 11 ? -2.929 -4.207 -0.916 1.00 92.27 11 A 1 ATOM 84 C CD1 . PHE A 1 11 ? -3.877 -5.051 -0.367 1.00 90.33 11 A 1 ATOM 85 C CD2 . PHE A 1 11 ? -2.755 -4.191 -2.291 1.00 90.80 11 A 1 ATOM 86 C CE1 . PHE A 1 11 ? -4.643 -5.876 -1.176 1.00 89.87 11 A 1 ATOM 87 C CE2 . PHE A 1 11 ? -3.516 -5.018 -3.105 1.00 89.60 11 A 1 ATOM 88 C CZ . PHE A 1 11 ? -4.462 -5.860 -2.545 1.00 90.06 11 A 1 ATOM 89 N N . SER A 1 12 ? 1.007 -3.592 -0.536 1.00 97.16 12 A 1 ATOM 90 C CA . SER A 1 12 ? 2.118 -3.866 -1.443 1.00 97.20 12 A 1 ATOM 91 C C . SER A 1 12 ? 2.981 -5.000 -0.904 1.00 97.51 12 A 1 ATOM 92 O O . SER A 1 12 ? 3.460 -5.844 -1.660 1.00 96.79 12 A 1 ATOM 93 C CB . SER A 1 12 ? 2.965 -2.609 -1.630 1.00 96.55 12 A 1 ATOM 94 O OG . SER A 1 12 ? 3.978 -2.830 -2.576 1.00 89.20 12 A 1 ATOM 95 N N . ALA A 1 13 ? 3.173 -5.011 0.402 1.00 97.29 13 A 1 ATOM 96 C CA . ALA A 1 13 ? 3.968 -6.051 1.052 1.00 97.33 13 A 1 ATOM 97 C C . ALA A 1 13 ? 3.274 -7.405 0.952 1.00 97.80 13 A 1 ATOM 98 O O . ALA A 1 13 ? 3.923 -8.432 0.752 1.00 96.70 13 A 1 ATOM 99 C CB . ALA A 1 13 ? 4.208 -5.681 2.511 1.00 96.44 13 A 1 ATOM 100 N N . VAL A 1 14 ? 1.954 -7.398 1.093 1.00 97.84 14 A 1 ATOM 101 C CA . VAL A 1 14 ? 1.163 -8.626 1.009 1.00 97.70 14 A 1 ATOM 102 C C . VAL A 1 14 ? 1.223 -9.199 -0.397 1.00 97.92 14 A 1 ATOM 103 O O . VAL A 1 14 ? 1.308 -10.417 -0.581 1.00 97.25 14 A 1 ATOM 104 C CB . VAL A 1 14 ? -0.297 -8.365 1.410 1.00 96.86 14 A 1 ATOM 105 C CG1 . VAL A 1 14 ? -1.119 -9.635 1.276 1.00 93.71 14 A 1 ATOM 106 C CG2 . VAL A 1 14 ? -0.367 -7.845 2.831 1.00 94.01 14 A 1 ATOM 107 N N . ALA A 1 15 ? 1.173 -8.320 -1.384 1.00 97.52 15 A 1 ATOM 108 C CA . ALA A 1 15 ? 1.226 -8.738 -2.781 1.00 97.44 15 A 1 ATOM 109 C C . ALA A 1 15 ? 2.578 -9.363 -3.114 1.00 97.63 15 A 1 ATOM 110 O O . ALA A 1 15 ? 2.661 -10.291 -3.919 1.00 96.58 15 A 1 ATOM 111 C CB . ALA A 1 15 ? 0.960 -7.543 -3.687 1.00 96.59 15 A 1 ATOM 112 N N . LEU A 1 16 ? 3.625 -8.841 -2.495 1.00 96.52 16 A 1 ATOM 113 C CA . LEU A 1 16 ? 4.975 -9.354 -2.709 1.00 95.93 16 A 1 ATOM 114 C C . LEU A 1 16 ? 5.158 -10.708 -2.041 1.00 96.16 16 A 1 ATOM 115 O O . LEU A 1 16 ? 5.757 -11.623 -2.613 1.00 94.71 16 A 1 ATOM 116 C CB . LEU A 1 16 ? 5.997 -8.351 -2.168 1.00 94.63 16 A 1 ATOM 117 C CG . LEU A 1 16 ? 6.891 -7.739 -3.241 1.00 89.85 16 A 1 ATOM 118 C CD1 . LEU A 1 16 ? 7.485 -6.427 -2.764 1.00 85.69 16 A 1 ATOM 119 C CD2 . LEU A 1 16 ? 7.993 -8.715 -3.620 1.00 83.40 16 A 1 ATOM 120 N N . ALA A 1 17 ? 4.642 -10.815 -0.834 1.00 94.64 17 A 1 ATOM 121 C CA . ALA A 1 17 ? 4.743 -12.046 -0.053 1.00 92.47 17 A 1 ATOM 122 C C . ALA A 1 17 ? 3.444 -12.838 -0.137 1.00 90.76 17 A 1 ATOM 123 O O . ALA A 1 17 ? 2.506 -12.540 0.612 1.00 86.73 17 A 1 ATOM 124 C CB . ALA A 1 17 ? 5.078 -11.722 1.392 1.00 88.23 17 A 1 ATOM 125 O OXT . ALA A 1 17 ? 3.356 -13.744 -0.960 1.00 80.84 17 A 1 #