# 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_spkb27734 # _entry.id spkb27734 # 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 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" "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 LEU 4 1 n THR 5 1 n VAL 6 1 n ALA 7 1 n ALA 8 1 n VAL 9 1 n PHE 10 1 n PHE 11 1 n THR 12 1 n ALA 13 1 n VAL 14 1 n LEU 15 1 n ALA 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 05:46:56)" _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 94.24 _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 86.18 1 1 A LYS 2 2 90.44 1 2 A PHE 3 2 92.55 1 3 A LEU 4 2 93.59 1 4 A THR 5 2 95.10 1 5 A VAL 6 2 96.97 1 6 A ALA 7 2 97.39 1 7 A ALA 8 2 97.68 1 8 A VAL 9 2 97.27 1 9 A PHE 10 2 94.62 1 10 A PHE 11 2 94.07 1 11 A THR 12 2 95.16 1 12 A ALA 13 2 97.61 1 13 A VAL 14 2 96.95 1 14 A LEU 15 2 94.10 1 15 A ALA 16 2 96.96 1 16 A ALA 17 2 92.04 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 LEU . 4 A 4 A 5 1 n THR . 5 A 5 A 6 1 n VAL . 6 A 6 A 7 1 n ALA . 7 A 7 A 8 1 n ALA . 8 A 8 A 9 1 n VAL . 9 A 9 A 10 1 n PHE . 10 A 10 A 11 1 n PHE . 11 A 11 A 12 1 n THR . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n VAL . 14 A 14 A 15 1 n LEU . 15 A 15 A 16 1 n ALA . 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 ? -8.385 -1.473 13.483 1.00 90.84 1 A 1 ATOM 2 C CA . MET A 1 1 ? -7.641 -0.994 12.310 1.00 92.08 1 A 1 ATOM 3 C C . MET A 1 1 ? -8.187 -1.615 11.033 1.00 93.05 1 A 1 ATOM 4 O O . MET A 1 1 ? -8.493 -2.804 11.002 1.00 90.20 1 A 1 ATOM 5 C CB . MET A 1 1 ? -6.159 -1.358 12.420 1.00 87.49 1 A 1 ATOM 6 C CG . MET A 1 1 ? -5.503 -0.794 13.661 1.00 84.30 1 A 1 ATOM 7 S SD . MET A 1 1 ? -3.772 -1.291 13.796 1.00 80.27 1 A 1 ATOM 8 C CE . MET A 1 1 ? -3.367 -0.584 15.382 1.00 71.17 1 A 1 ATOM 9 N N . LYS A 1 2 ? -8.312 -0.819 9.990 1.00 95.27 2 A 1 ATOM 10 C CA . LYS A 1 2 ? -8.815 -1.312 8.715 1.00 95.70 2 A 1 ATOM 11 C C . LYS A 1 2 ? -7.668 -1.866 7.871 1.00 96.33 2 A 1 ATOM 12 O O . LYS A 1 2 ? -6.533 -1.414 7.980 1.00 96.07 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -9.518 -0.187 7.954 1.00 94.52 2 A 1 ATOM 14 C CG . LYS A 1 2 ? -10.802 0.275 8.614 1.00 90.16 2 A 1 ATOM 15 C CD . LYS A 1 2 ? -11.472 1.362 7.788 1.00 87.47 2 A 1 ATOM 16 C CE . LYS A 1 2 ? -12.762 1.824 8.437 1.00 82.25 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? -13.395 2.916 7.646 1.00 76.16 2 A 1 ATOM 18 N N . PHE A 1 3 ? -7.974 -2.833 7.027 1.00 94.23 3 A 1 ATOM 19 C CA . PHE A 1 3 ? -6.983 -3.428 6.136 1.00 95.29 3 A 1 ATOM 20 C C . PHE A 1 3 ? -6.565 -2.437 5.052 1.00 96.66 3 A 1 ATOM 21 O O . PHE A 1 3 ? -5.481 -2.558 4.478 1.00 96.02 3 A 1 ATOM 22 C CB . PHE A 1 3 ? -7.544 -4.706 5.512 1.00 94.53 3 A 1 ATOM 23 C CG . PHE A 1 3 ? -9.010 -4.606 5.165 1.00 92.83 3 A 1 ATOM 24 C CD1 . PHE A 1 3 ? -9.419 -3.968 4.004 1.00 90.64 3 A 1 ATOM 25 C CD2 . PHE A 1 3 ? -9.966 -5.138 6.016 1.00 90.39 3 A 1 ATOM 26 C CE1 . PHE A 1 3 ? -10.764 -3.867 3.683 1.00 89.49 3 A 1 ATOM 27 C CE2 . PHE A 1 3 ? -11.322 -5.037 5.700 1.00 89.35 3 A 1 ATOM 28 C CZ . PHE A 1 3 ? -11.717 -4.402 4.531 1.00 88.63 3 A 1 ATOM 29 N N . LEU A 1 4 ? -7.420 -1.465 4.778 1.00 95.87 4 A 1 ATOM 30 C CA . LEU A 1 4 ? -7.145 -0.458 3.757 1.00 96.58 4 A 1 ATOM 31 C C . LEU A 1 4 ? -5.962 0.419 4.156 1.00 97.32 4 A 1 ATOM 32 O O . LEU A 1 4 ? -5.166 0.832 3.316 1.00 96.73 4 A 1 ATOM 33 C CB . LEU A 1 4 ? -8.389 0.411 3.541 1.00 95.84 4 A 1 ATOM 34 C CG . LEU A 1 4 ? -9.606 -0.349 3.016 1.00 91.18 4 A 1 ATOM 35 C CD1 . LEU A 1 4 ? -10.817 0.572 2.974 1.00 88.31 4 A 1 ATOM 36 C CD2 . LEU A 1 4 ? -9.330 -0.923 1.636 1.00 86.90 4 A 1 ATOM 37 N N . THR A 1 5 ? -5.840 0.699 5.437 1.00 95.54 5 A 1 ATOM 38 C CA . THR A 1 5 ? -4.756 1.534 5.947 1.00 96.42 5 A 1 ATOM 39 C C . THR A 1 5 ? -3.411 0.832 5.782 1.00 97.10 5 A 1 ATOM 40 O O . THR A 1 5 ? -2.434 1.430 5.331 1.00 96.82 5 A 1 ATOM 41 C CB . THR A 1 5 ? -4.972 1.869 7.426 1.00 96.24 5 A 1 ATOM 42 O OG1 . THR A 1 5 ? -6.266 2.435 7.613 1.00 92.69 5 A 1 ATOM 43 C CG2 . THR A 1 5 ? -3.918 2.858 7.909 1.00 90.90 5 A 1 ATOM 44 N N . VAL A 1 6 ? -3.356 -0.432 6.143 1.00 97.54 6 A 1 ATOM 45 C CA . VAL A 1 6 ? -2.126 -1.213 6.036 1.00 97.74 6 A 1 ATOM 46 C C . VAL A 1 6 ? -1.720 -1.373 4.576 1.00 97.92 6 A 1 ATOM 47 O O . VAL A 1 6 ? -0.538 -1.296 4.234 1.00 97.78 6 A 1 ATOM 48 C CB . VAL A 1 6 ? -2.303 -2.595 6.676 1.00 97.37 6 A 1 ATOM 49 C CG1 . VAL A 1 6 ? -1.028 -3.413 6.540 1.00 95.25 6 A 1 ATOM 50 C CG2 . VAL A 1 6 ? -2.689 -2.451 8.140 1.00 95.21 6 A 1 ATOM 51 N N . ALA A 1 7 ? -2.706 -1.588 3.721 1.00 97.48 7 A 1 ATOM 52 C CA . ALA A 1 7 ? -2.451 -1.760 2.296 1.00 97.46 7 A 1 ATOM 53 C C . ALA A 1 7 ? -1.868 -0.493 1.680 1.00 97.72 7 A 1 ATOM 54 O O . ALA A 1 7 ? -0.984 -0.560 0.827 1.00 97.34 7 A 1 ATOM 55 C CB . ALA A 1 7 ? -3.750 -2.127 1.584 1.00 96.95 7 A 1 ATOM 56 N N . ALA A 1 8 ? -2.363 0.663 2.108 1.00 97.60 8 A 1 ATOM 57 C CA . ALA A 1 8 ? -1.892 1.942 1.587 1.00 97.79 8 A 1 ATOM 58 C C . ALA A 1 8 ? -0.425 2.171 1.936 1.00 98.04 8 A 1 ATOM 59 O O . ALA A 1 8 ? 0.354 2.630 1.101 1.00 97.54 8 A 1 ATOM 60 C CB . ALA A 1 8 ? -2.746 3.074 2.145 1.00 97.41 8 A 1 ATOM 61 N N . VAL A 1 9 ? -0.042 1.856 3.165 1.00 97.75 9 A 1 ATOM 62 C CA . VAL A 1 9 ? 1.338 2.028 3.616 1.00 97.83 9 A 1 ATOM 63 C C . VAL A 1 9 ? 2.270 1.091 2.856 1.00 98.03 9 A 1 ATOM 64 O O . VAL A 1 9 ? 3.352 1.486 2.414 1.00 97.78 9 A 1 ATOM 65 C CB . VAL A 1 9 ? 1.457 1.769 5.126 1.00 97.52 9 A 1 ATOM 66 C CG1 . VAL A 1 9 ? 2.910 1.864 5.577 1.00 96.21 9 A 1 ATOM 67 C CG2 . VAL A 1 9 ? 0.605 2.764 5.899 1.00 95.75 9 A 1 ATOM 68 N N . PHE A 1 10 ? 1.845 -0.147 2.711 1.00 97.24 10 A 1 ATOM 69 C CA . PHE A 1 10 ? 2.646 -1.142 2.005 1.00 96.94 10 A 1 ATOM 70 C C . PHE A 1 10 ? 2.803 -0.779 0.530 1.00 97.26 10 A 1 ATOM 71 O O . PHE A 1 10 ? 3.887 -0.902 -0.042 1.00 97.14 10 A 1 ATOM 72 C CB . PHE A 1 10 ? 1.989 -2.517 2.137 1.00 96.54 10 A 1 ATOM 73 C CG . PHE A 1 10 ? 2.805 -3.611 1.504 1.00 94.89 10 A 1 ATOM 74 C CD1 . PHE A 1 10 ? 3.949 -4.085 2.134 1.00 92.45 10 A 1 ATOM 75 C CD2 . PHE A 1 10 ? 2.430 -4.156 0.287 1.00 92.94 10 A 1 ATOM 76 C CE1 . PHE A 1 10 ? 4.711 -5.089 1.554 1.00 91.61 10 A 1 ATOM 77 C CE2 . PHE A 1 10 ? 3.191 -5.161 -0.302 1.00 91.83 10 A 1 ATOM 78 C CZ . PHE A 1 10 ? 4.332 -5.626 0.333 1.00 91.98 10 A 1 ATOM 79 N N . PHE A 1 11 ? 1.710 -0.328 -0.081 1.00 96.66 11 A 1 ATOM 80 C CA . PHE A 1 11 ? 1.723 0.042 -1.494 1.00 96.53 11 A 1 ATOM 81 C C . PHE A 1 11 ? 2.659 1.219 -1.740 1.00 97.14 11 A 1 ATOM 82 O O . PHE A 1 11 ? 3.359 1.275 -2.752 1.00 96.83 11 A 1 ATOM 83 C CB . PHE A 1 11 ? 0.305 0.397 -1.945 1.00 96.11 11 A 1 ATOM 84 C CG . PHE A 1 11 ? 0.045 -0.002 -3.373 1.00 93.98 11 A 1 ATOM 85 C CD1 . PHE A 1 11 ? 0.493 0.786 -4.422 1.00 92.01 11 A 1 ATOM 86 C CD2 . PHE A 1 11 ? -0.646 -1.172 -3.660 1.00 92.35 11 A 1 ATOM 87 C CE1 . PHE A 1 11 ? 0.264 0.417 -5.739 1.00 91.06 11 A 1 ATOM 88 C CE2 . PHE A 1 11 ? -0.883 -1.545 -4.975 1.00 90.89 11 A 1 ATOM 89 C CZ . PHE A 1 11 ? -0.426 -0.751 -6.015 1.00 91.19 11 A 1 ATOM 90 N N . THR A 1 12 ? 2.681 2.161 -0.805 1.00 96.96 12 A 1 ATOM 91 C CA . THR A 1 12 ? 3.541 3.340 -0.919 1.00 96.59 12 A 1 ATOM 92 C C . THR A 1 12 ? 5.011 2.928 -0.947 1.00 97.12 12 A 1 ATOM 93 O O . THR A 1 12 ? 5.812 3.487 -1.697 1.00 96.41 12 A 1 ATOM 94 C CB . THR A 1 12 ? 3.310 4.296 0.256 1.00 96.03 12 A 1 ATOM 95 O OG1 . THR A 1 12 ? 1.934 4.663 0.318 1.00 92.02 12 A 1 ATOM 96 C CG2 . THR A 1 12 ? 4.152 5.557 0.098 1.00 91.01 12 A 1 ATOM 97 N N . ALA A 1 13 ? 5.363 1.950 -0.123 1.00 97.72 13 A 1 ATOM 98 C CA . ALA A 1 13 ? 6.739 1.465 -0.052 1.00 97.67 13 A 1 ATOM 99 C C . ALA A 1 13 ? 7.168 0.830 -1.373 1.00 98.03 13 A 1 ATOM 100 O O . ALA A 1 13 ? 8.312 0.982 -1.805 1.00 97.42 13 A 1 ATOM 101 C CB . ALA A 1 13 ? 6.874 0.458 1.085 1.00 97.22 13 A 1 ATOM 102 N N . VAL A 1 14 ? 6.253 0.128 -2.015 1.00 97.93 14 A 1 ATOM 103 C CA . VAL A 1 14 ? 6.540 -0.520 -3.295 1.00 97.88 14 A 1 ATOM 104 C C . VAL A 1 14 ? 6.799 0.512 -4.385 1.00 98.01 14 A 1 ATOM 105 O O . VAL A 1 14 ? 7.715 0.361 -5.198 1.00 97.51 14 A 1 ATOM 106 C CB . VAL A 1 14 ? 5.379 -1.437 -3.713 1.00 97.34 14 A 1 ATOM 107 C CG1 . VAL A 1 14 ? 5.656 -2.059 -5.075 1.00 95.09 14 A 1 ATOM 108 C CG2 . VAL A 1 14 ? 5.170 -2.524 -2.674 1.00 94.86 14 A 1 ATOM 109 N N . LEU A 1 15 ? 5.990 1.566 -4.405 1.00 97.30 15 A 1 ATOM 110 C CA . LEU A 1 15 ? 6.129 2.618 -5.408 1.00 96.92 15 A 1 ATOM 111 C C . LEU A 1 15 ? 7.397 3.433 -5.179 1.00 97.13 15 A 1 ATOM 112 O O . LEU A 1 15 ? 8.002 3.930 -6.129 1.00 96.93 15 A 1 ATOM 113 C CB . LEU A 1 15 ? 4.907 3.540 -5.360 1.00 96.27 15 A 1 ATOM 114 C CG . LEU A 1 15 ? 3.602 2.868 -5.788 1.00 91.85 15 A 1 ATOM 115 C CD1 . LEU A 1 15 ? 2.427 3.803 -5.545 1.00 88.64 15 A 1 ATOM 116 C CD2 . LEU A 1 15 ? 3.663 2.470 -7.256 1.00 87.79 15 A 1 ATOM 117 N N . ALA A 1 16 ? 7.798 3.590 -3.925 1.00 97.27 16 A 1 ATOM 118 C CA . ALA A 1 16 ? 8.994 4.352 -3.568 1.00 97.17 16 A 1 ATOM 119 C C . ALA A 1 16 ? 10.269 3.600 -3.928 1.00 97.43 16 A 1 ATOM 120 O O . ALA A 1 16 ? 11.309 4.210 -4.179 1.00 96.67 16 A 1 ATOM 121 C CB . ALA A 1 16 ? 8.984 4.675 -2.078 1.00 96.27 16 A 1 ATOM 122 N N . ALA A 1 17 ? 10.199 2.277 -3.954 1.00 96.34 17 A 1 ATOM 123 C CA . ALA A 1 17 ? 11.352 1.446 -4.251 1.00 94.98 17 A 1 ATOM 124 C C . ALA A 1 17 ? 11.744 1.545 -5.724 1.00 93.60 17 A 1 ATOM 125 O O . ALA A 1 17 ? 10.864 1.774 -6.571 1.00 90.68 17 A 1 ATOM 126 C CB . ALA A 1 17 ? 11.074 -0.003 -3.860 1.00 92.28 17 A 1 ATOM 127 O OXT . ALA A 1 17 ? 12.925 1.376 -6.043 1.00 84.36 17 A 1 #