# 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_spkb20395 # _entry.id spkb20395 # 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" "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" "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 LEU 2 1 n GLN 3 1 n LYS 4 1 n THR 5 1 n VAL 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 GLN 14 1 n VAL 15 1 n LEU 16 1 n MET 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 @ 2025-07-08 14:54:18)" _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 94.81 _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 88.78 1 1 A LEU 2 2 94.33 1 2 A GLN 3 2 93.93 1 3 A LYS 4 2 93.51 1 4 A THR 5 2 96.47 1 5 A VAL 6 2 97.58 1 6 A LEU 7 2 95.89 1 7 A LEU 8 2 95.70 1 8 A LEU 9 2 96.14 1 9 A ALA 10 2 98.47 1 10 A LEU 11 2 96.41 1 11 A VAL 12 2 97.82 1 12 A ALA 13 2 98.21 1 13 A GLN 14 2 93.91 1 14 A VAL 15 2 96.65 1 15 A LEU 16 2 94.81 1 16 A MET 17 2 88.14 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 LEU . 2 A 2 A 3 1 n GLN . 3 A 3 A 4 1 n LYS . 4 A 4 A 5 1 n THR . 5 A 5 A 6 1 n VAL . 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 GLN . 14 A 14 A 15 1 n VAL . 15 A 15 A 16 1 n LEU . 16 A 16 A 17 1 n MET . 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 ? -13.689 0.647 0.717 1.00 92.65 1 A 1 ATOM 2 C CA . MET A 1 1 ? -13.080 1.981 0.915 1.00 94.35 1 A 1 ATOM 3 C C . MET A 1 1 ? -11.922 2.180 -0.055 1.00 95.83 1 A 1 ATOM 4 O O . MET A 1 1 ? -11.095 1.290 -0.207 1.00 94.69 1 A 1 ATOM 5 C CB . MET A 1 1 ? -12.571 2.120 2.350 1.00 90.70 1 A 1 ATOM 6 C CG . MET A 1 1 ? -13.713 2.304 3.342 1.00 85.66 1 A 1 ATOM 7 S SD . MET A 1 1 ? -13.102 2.465 5.028 1.00 83.38 1 A 1 ATOM 8 C CE . MET A 1 1 ? -14.638 2.772 5.882 1.00 73.02 1 A 1 ATOM 9 N N . LEU A 1 2 ? -11.876 3.330 -0.703 1.00 96.05 2 A 1 ATOM 10 C CA . LEU A 1 2 ? -10.818 3.628 -1.672 1.00 97.23 2 A 1 ATOM 11 C C . LEU A 1 2 ? -9.491 3.931 -0.975 1.00 97.97 2 A 1 ATOM 12 O O . LEU A 1 2 ? -8.427 3.606 -1.497 1.00 97.47 2 A 1 ATOM 13 C CB . LEU A 1 2 ? -11.246 4.819 -2.533 1.00 96.49 2 A 1 ATOM 14 C CG . LEU A 1 2 ? -12.514 4.568 -3.347 1.00 92.57 2 A 1 ATOM 15 C CD1 . LEU A 1 2 ? -13.644 5.463 -2.863 1.00 89.36 2 A 1 ATOM 16 C CD2 . LEU A 1 2 ? -12.245 4.834 -4.823 1.00 87.47 2 A 1 ATOM 17 N N . GLN A 1 3 ? -9.560 4.539 0.199 1.00 97.76 3 A 1 ATOM 18 C CA . GLN A 1 3 ? -8.352 4.901 0.948 1.00 98.08 3 A 1 ATOM 19 C C . GLN A 1 3 ? -7.525 3.670 1.314 1.00 98.31 3 A 1 ATOM 20 O O . GLN A 1 3 ? -6.302 3.686 1.202 1.00 97.78 3 A 1 ATOM 21 C CB . GLN A 1 3 ? -8.740 5.675 2.211 1.00 97.45 3 A 1 ATOM 22 C CG . GLN A 1 3 ? -8.480 7.167 2.064 1.00 93.69 3 A 1 ATOM 23 C CD . GLN A 1 3 ? -7.809 7.731 3.308 1.00 91.71 3 A 1 ATOM 24 O OE1 . GLN A 1 3 ? -6.852 7.180 3.825 1.00 86.19 3 A 1 ATOM 25 N NE2 . GLN A 1 3 ? -8.308 8.832 3.822 1.00 84.42 3 A 1 ATOM 26 N N . LYS A 1 4 ? -8.184 2.594 1.728 1.00 97.97 4 A 1 ATOM 27 C CA . LYS A 1 4 ? -7.482 1.362 2.099 1.00 98.24 4 A 1 ATOM 28 C C . LYS A 1 4 ? -6.786 0.745 0.892 1.00 98.43 4 A 1 ATOM 29 O O . LYS A 1 4 ? -5.673 0.239 1.012 1.00 98.23 4 A 1 ATOM 30 C CB . LYS A 1 4 ? -8.471 0.370 2.722 1.00 97.96 4 A 1 ATOM 31 C CG . LYS A 1 4 ? -8.686 0.632 4.213 1.00 94.24 4 A 1 ATOM 32 C CD . LYS A 1 4 ? -7.498 0.139 5.037 1.00 90.99 4 A 1 ATOM 33 C CE . LYS A 1 4 ? -7.743 0.285 6.530 1.00 86.10 4 A 1 ATOM 34 N NZ . LYS A 1 4 ? -6.559 -0.146 7.314 1.00 79.45 4 A 1 ATOM 35 N N . THR A 1 5 ? -7.419 0.807 -0.253 1.00 97.92 5 A 1 ATOM 36 C CA . THR A 1 5 ? -6.846 0.265 -1.481 1.00 98.02 5 A 1 ATOM 37 C C . THR A 1 5 ? -5.601 1.050 -1.884 1.00 98.25 5 A 1 ATOM 38 O O . THR A 1 5 ? -4.596 0.463 -2.286 1.00 97.97 5 A 1 ATOM 39 C CB . THR A 1 5 ? -7.877 0.302 -2.611 1.00 97.69 5 A 1 ATOM 40 O OG1 . THR A 1 5 ? -9.115 -0.221 -2.148 1.00 93.42 5 A 1 ATOM 41 C CG2 . THR A 1 5 ? -7.416 -0.536 -3.793 1.00 92.03 5 A 1 ATOM 42 N N . VAL A 1 6 ? -5.658 2.358 -1.766 1.00 98.26 6 A 1 ATOM 43 C CA . VAL A 1 6 ? -4.527 3.223 -2.106 1.00 98.33 6 A 1 ATOM 44 C C . VAL A 1 6 ? -3.368 2.977 -1.140 1.00 98.45 6 A 1 ATOM 45 O O . VAL A 1 6 ? -2.207 2.946 -1.547 1.00 98.22 6 A 1 ATOM 46 C CB . VAL A 1 6 ? -4.950 4.706 -2.083 1.00 98.01 6 A 1 ATOM 47 C CG1 . VAL A 1 6 ? -3.760 5.623 -2.330 1.00 96.04 6 A 1 ATOM 48 C CG2 . VAL A 1 6 ? -6.018 4.964 -3.141 1.00 95.72 6 A 1 ATOM 49 N N . LEU A 1 7 ? -3.695 2.786 0.133 1.00 98.22 7 A 1 ATOM 50 C CA . LEU A 1 7 ? -2.684 2.529 1.156 1.00 98.23 7 A 1 ATOM 51 C C . LEU A 1 7 ? -1.964 1.210 0.888 1.00 98.42 7 A 1 ATOM 52 O O . LEU A 1 7 ? -0.742 1.124 1.019 1.00 98.37 7 A 1 ATOM 53 C CB . LEU A 1 7 ? -3.345 2.495 2.539 1.00 98.06 7 A 1 ATOM 54 C CG . LEU A 1 7 ? -2.442 3.039 3.645 1.00 92.88 7 A 1 ATOM 55 C CD1 . LEU A 1 7 ? -2.898 4.434 4.063 1.00 91.01 7 A 1 ATOM 56 C CD2 . LEU A 1 7 ? -2.442 2.120 4.847 1.00 91.91 7 A 1 ATOM 57 N N . LEU A 1 8 ? -2.721 0.198 0.497 1.00 98.22 8 A 1 ATOM 58 C CA . LEU A 1 8 ? -2.150 -1.111 0.181 1.00 98.25 8 A 1 ATOM 59 C C . LEU A 1 8 ? -1.208 -1.019 -1.013 1.00 98.46 8 A 1 ATOM 60 O O . LEU A 1 8 ? -0.128 -1.613 -1.006 1.00 98.45 8 A 1 ATOM 61 C CB . LEU A 1 8 ? -3.287 -2.100 -0.101 1.00 98.04 8 A 1 ATOM 62 C CG . LEU A 1 8 ? -3.581 -3.016 1.089 1.00 91.51 8 A 1 ATOM 63 C CD1 . LEU A 1 8 ? -5.060 -3.326 1.201 1.00 90.89 8 A 1 ATOM 64 C CD2 . LEU A 1 8 ? -2.790 -4.316 0.940 1.00 91.78 8 A 1 ATOM 65 N N . LEU A 1 9 ? -1.610 -0.268 -2.017 1.00 98.33 9 A 1 ATOM 66 C CA . LEU A 1 9 ? -0.785 -0.084 -3.209 1.00 98.25 9 A 1 ATOM 67 C C . LEU A 1 9 ? 0.525 0.615 -2.858 1.00 98.45 9 A 1 ATOM 68 O O . LEU A 1 9 ? 1.592 0.227 -3.341 1.00 98.34 9 A 1 ATOM 69 C CB . LEU A 1 9 ? -1.557 0.732 -4.249 1.00 97.83 9 A 1 ATOM 70 C CG . LEU A 1 9 ? -1.587 0.063 -5.622 1.00 93.21 9 A 1 ATOM 71 C CD1 . LEU A 1 9 ? -2.904 -0.667 -5.840 1.00 92.26 9 A 1 ATOM 72 C CD2 . LEU A 1 9 ? -1.378 1.087 -6.719 1.00 92.43 9 A 1 ATOM 73 N N . ALA A 1 10 ? 0.436 1.633 -2.010 1.00 98.57 10 A 1 ATOM 74 C CA . ALA A 1 10 ? 1.618 2.380 -1.589 1.00 98.53 10 A 1 ATOM 75 C C . ALA A 1 10 ? 2.566 1.489 -0.781 1.00 98.63 10 A 1 ATOM 76 O O . ALA A 1 10 ? 3.785 1.580 -0.929 1.00 98.34 10 A 1 ATOM 77 C CB . ALA A 1 10 ? 1.184 3.594 -0.769 1.00 98.30 10 A 1 ATOM 78 N N . LEU A 1 11 ? 2.003 0.623 0.050 1.00 98.50 11 A 1 ATOM 79 C CA . LEU A 1 11 ? 2.793 -0.294 0.866 1.00 98.43 11 A 1 ATOM 80 C C . LEU A 1 11 ? 3.533 -1.299 -0.009 1.00 98.59 11 A 1 ATOM 81 O O . LEU A 1 11 ? 4.717 -1.565 0.209 1.00 98.33 11 A 1 ATOM 82 C CB . LEU A 1 11 ? 1.879 -1.021 1.853 1.00 98.16 11 A 1 ATOM 83 C CG . LEU A 1 11 ? 2.610 -1.472 3.115 1.00 94.21 11 A 1 ATOM 84 C CD1 . LEU A 1 11 ? 2.106 -0.700 4.325 1.00 92.23 11 A 1 ATOM 85 C CD2 . LEU A 1 11 ? 2.433 -2.958 3.347 1.00 92.83 11 A 1 ATOM 86 N N . VAL A 1 12 ? 2.847 -1.842 -0.993 1.00 98.56 12 A 1 ATOM 87 C CA . VAL A 1 12 ? 3.448 -2.807 -1.913 1.00 98.51 12 A 1 ATOM 88 C C . VAL A 1 12 ? 4.589 -2.156 -2.688 1.00 98.57 12 A 1 ATOM 89 O O . VAL A 1 12 ? 5.648 -2.764 -2.873 1.00 98.19 12 A 1 ATOM 90 C CB . VAL A 1 12 ? 2.385 -3.373 -2.875 1.00 98.11 12 A 1 ATOM 91 C CG1 . VAL A 1 12 ? 3.019 -4.256 -3.940 1.00 96.15 12 A 1 ATOM 92 C CG2 . VAL A 1 12 ? 1.349 -4.182 -2.106 1.00 96.64 12 A 1 ATOM 93 N N . ALA A 1 13 ? 4.380 -0.935 -3.127 1.00 98.50 13 A 1 ATOM 94 C CA . ALA A 1 13 ? 5.401 -0.197 -3.868 1.00 98.37 13 A 1 ATOM 95 C C . ALA A 1 13 ? 6.628 0.080 -2.996 1.00 98.46 13 A 1 ATOM 96 O O . ALA A 1 13 ? 7.760 0.019 -3.475 1.00 97.85 13 A 1 ATOM 97 C CB . ALA A 1 13 ? 4.809 1.109 -4.388 1.00 97.89 13 A 1 ATOM 98 N N . GLN A 1 14 ? 6.401 0.362 -1.720 1.00 98.61 14 A 1 ATOM 99 C CA . GLN A 1 14 ? 7.497 0.624 -0.782 1.00 98.52 14 A 1 ATOM 100 C C . GLN A 1 14 ? 8.291 -0.644 -0.486 1.00 98.61 14 A 1 ATOM 101 O O . GLN A 1 14 ? 9.518 -0.600 -0.406 1.00 97.79 14 A 1 ATOM 102 C CB . GLN A 1 14 ? 6.948 1.203 0.520 1.00 98.10 14 A 1 ATOM 103 C CG . GLN A 1 14 ? 7.012 2.723 0.526 1.00 94.07 14 A 1 ATOM 104 C CD . GLN A 1 14 ? 6.789 3.280 1.916 1.00 91.05 14 A 1 ATOM 105 O OE1 . GLN A 1 14 ? 5.923 2.821 2.648 1.00 85.56 14 A 1 ATOM 106 N NE2 . GLN A 1 14 ? 7.561 4.274 2.313 1.00 82.91 14 A 1 ATOM 107 N N . VAL A 1 15 ? 7.607 -1.752 -0.330 1.00 98.16 15 A 1 ATOM 108 C CA . VAL A 1 15 ? 8.265 -3.032 -0.051 1.00 98.02 15 A 1 ATOM 109 C C . VAL A 1 15 ? 9.100 -3.479 -1.248 1.00 98.19 15 A 1 ATOM 110 O O . VAL A 1 15 ? 10.186 -4.040 -1.079 1.00 97.07 15 A 1 ATOM 111 C CB . VAL A 1 15 ? 7.224 -4.106 0.320 1.00 97.33 15 A 1 ATOM 112 C CG1 . VAL A 1 15 ? 7.865 -5.482 0.443 1.00 93.78 15 A 1 ATOM 113 C CG2 . VAL A 1 15 ? 6.549 -3.755 1.638 1.00 93.99 15 A 1 ATOM 114 N N . LEU A 1 16 ? 8.603 -3.240 -2.438 1.00 97.70 16 A 1 ATOM 115 C CA . LEU A 1 16 ? 9.310 -3.610 -3.663 1.00 97.49 16 A 1 ATOM 116 C C . LEU A 1 16 ? 10.490 -2.685 -3.933 1.00 97.48 16 A 1 ATOM 117 O O . LEU A 1 16 ? 11.480 -3.094 -4.545 1.00 96.12 16 A 1 ATOM 118 C CB . LEU A 1 16 ? 8.333 -3.588 -4.845 1.00 96.85 16 A 1 ATOM 119 C CG . LEU A 1 16 ? 8.549 -4.741 -5.821 1.00 93.88 16 A 1 ATOM 120 C CD1 . LEU A 1 16 ? 7.320 -5.639 -5.889 1.00 90.06 16 A 1 ATOM 121 C CD2 . LEU A 1 16 ? 8.882 -4.222 -7.208 1.00 88.86 16 A 1 ATOM 122 N N . MET A 1 17 ? 10.367 -1.450 -3.486 1.00 96.53 17 A 1 ATOM 123 C CA . MET A 1 17 ? 11.411 -0.447 -3.697 1.00 94.32 17 A 1 ATOM 124 C C . MET A 1 17 ? 12.551 -0.599 -2.693 1.00 92.91 17 A 1 ATOM 125 O O . MET A 1 17 ? 12.270 -0.742 -1.496 1.00 90.43 17 A 1 ATOM 126 C CB . MET A 1 17 ? 10.817 0.961 -3.607 1.00 90.05 17 A 1 ATOM 127 C CG . MET A 1 17 ? 11.496 1.923 -4.563 1.00 85.47 17 A 1 ATOM 128 S SD . MET A 1 17 ? 11.118 3.652 -4.221 1.00 85.26 17 A 1 ATOM 129 C CE . MET A 1 17 ? 12.435 4.016 -3.074 1.00 76.26 17 A 1 ATOM 130 O OXT . MET A 1 17 ? 13.717 -0.574 -3.119 1.00 82.07 17 A 1 #