# 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_spkb36463 # _entry.id spkb36463 # 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" "C3 H7 N O2 S" 121.158 CYS y CYSTEINE C([C@@H](C(=O)O)N)S ? "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" "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 GLY 3 1 n LEU 4 1 n CYS 5 1 n VAL 6 1 n ALA 7 1 n ALA 8 1 n CYS 9 1 n THR 10 1 n LEU 11 1 n VAL 12 1 n LEU 13 1 n ALA 14 1 n ALA 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 @ 2025-07-05 20:16:55)" _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 95.60 _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 89.56 1 1 A LYS 2 2 91.04 1 2 A GLY 3 2 96.99 1 3 A LEU 4 2 96.17 1 4 A CYS 5 2 96.83 1 5 A VAL 6 2 97.75 1 6 A ALA 7 2 98.19 1 7 A ALA 8 2 98.14 1 8 A CYS 9 2 96.90 1 9 A THR 10 2 96.74 1 10 A LEU 11 2 96.20 1 11 A VAL 12 2 97.64 1 12 A LEU 13 2 95.98 1 13 A ALA 14 2 97.87 1 14 A ALA 15 2 97.14 1 15 A ALA 16 2 91.23 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 LYS . 2 A 2 A 3 1 n GLY . 3 A 3 A 4 1 n LEU . 4 A 4 A 5 1 n CYS . 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 CYS . 9 A 9 A 10 1 n THR . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n VAL . 12 A 12 A 13 1 n LEU . 13 A 13 A 14 1 n ALA . 14 A 14 A 15 1 n ALA . 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 ? 2.790 0.716 12.511 1.00 93.42 1 A 1 ATOM 2 C CA . MET A 1 1 ? 1.698 1.435 11.832 1.00 93.89 1 A 1 ATOM 3 C C . MET A 1 1 ? 1.421 0.794 10.472 1.00 94.81 1 A 1 ATOM 4 O O . MET A 1 1 ? 1.926 1.244 9.448 1.00 92.58 1 A 1 ATOM 5 C CB . MET A 1 1 ? 2.072 2.902 11.638 1.00 91.95 1 A 1 ATOM 6 C CG . MET A 1 1 ? 2.274 3.619 12.957 1.00 89.97 1 A 1 ATOM 7 S SD . MET A 1 1 ? 2.780 5.330 12.739 1.00 84.53 1 A 1 ATOM 8 C CE . MET A 1 1 ? 2.895 5.839 14.439 1.00 75.30 1 A 1 ATOM 9 N N . LYS A 1 2 ? 0.626 -0.267 10.484 1.00 95.07 2 A 1 ATOM 10 C CA . LYS A 1 2 ? 0.329 -1.008 9.261 1.00 96.16 2 A 1 ATOM 11 C C . LYS A 1 2 ? -0.763 -0.334 8.435 1.00 96.76 2 A 1 ATOM 12 O O . LYS A 1 2 ? -0.818 -0.529 7.225 1.00 95.96 2 A 1 ATOM 13 C CB . LYS A 1 2 ? -0.077 -2.444 9.609 1.00 94.99 2 A 1 ATOM 14 C CG . LYS A 1 2 ? 1.056 -3.253 10.224 1.00 90.66 2 A 1 ATOM 15 C CD . LYS A 1 2 ? 0.609 -4.666 10.556 1.00 87.88 2 A 1 ATOM 16 C CE . LYS A 1 2 ? 1.752 -5.475 11.153 1.00 83.27 2 A 1 ATOM 17 N NZ . LYS A 1 2 ? 1.305 -6.845 11.533 1.00 78.63 2 A 1 ATOM 18 N N . GLY A 1 3 ? -1.619 0.437 9.081 1.00 95.94 3 A 1 ATOM 19 C CA . GLY A 1 3 ? -2.737 1.085 8.398 1.00 96.90 3 A 1 ATOM 20 C C . GLY A 1 3 ? -2.299 1.928 7.213 1.00 97.80 3 A 1 ATOM 21 O O . GLY A 1 3 ? -2.885 1.856 6.131 1.00 97.33 3 A 1 ATOM 22 N N . LEU A 1 4 ? -1.246 2.719 7.405 1.00 97.36 4 A 1 ATOM 23 C CA . LEU A 1 4 ? -0.725 3.577 6.343 1.00 97.92 4 A 1 ATOM 24 C C . LEU A 1 4 ? -0.113 2.747 5.221 1.00 98.21 4 A 1 ATOM 25 O O . LEU A 1 4 ? -0.348 3.010 4.039 1.00 97.82 4 A 1 ATOM 26 C CB . LEU A 1 4 ? 0.316 4.540 6.916 1.00 97.84 4 A 1 ATOM 27 C CG . LEU A 1 4 ? -0.255 5.562 7.898 1.00 95.83 4 A 1 ATOM 28 C CD1 . LEU A 1 4 ? 0.868 6.347 8.546 1.00 92.31 4 A 1 ATOM 29 C CD2 . LEU A 1 4 ? -1.224 6.501 7.199 1.00 92.05 4 A 1 ATOM 30 N N . CYS A 1 5 ? 0.666 1.729 5.600 1.00 97.24 5 A 1 ATOM 31 C CA . CYS A 1 5 ? 1.306 0.854 4.628 1.00 97.61 5 A 1 ATOM 32 C C . CYS A 1 5 ? 0.268 0.076 3.827 1.00 97.85 5 A 1 ATOM 33 O O . CYS A 1 5 ? 0.380 -0.049 2.609 1.00 97.17 5 A 1 ATOM 34 C CB . CYS A 1 5 ? 2.259 -0.108 5.335 1.00 96.99 5 A 1 ATOM 35 S SG . CYS A 1 5 ? 3.647 0.749 6.113 1.00 94.11 5 A 1 ATOM 36 N N . VAL A 1 6 ? -0.741 -0.440 4.522 1.00 97.92 6 A 1 ATOM 37 C CA . VAL A 1 6 ? -1.809 -1.199 3.873 1.00 98.15 6 A 1 ATOM 38 C C . VAL A 1 6 ? -2.572 -0.313 2.897 1.00 98.28 6 A 1 ATOM 39 O O . VAL A 1 6 ? -2.870 -0.727 1.774 1.00 98.23 6 A 1 ATOM 40 C CB . VAL A 1 6 ? -2.769 -1.800 4.911 1.00 97.94 6 A 1 ATOM 41 C CG1 . VAL A 1 6 ? -3.985 -2.422 4.240 1.00 96.96 6 A 1 ATOM 42 C CG2 . VAL A 1 6 ? -2.042 -2.850 5.737 1.00 96.80 6 A 1 ATOM 43 N N . ALA A 1 7 ? -2.875 0.899 3.318 1.00 98.13 7 A 1 ATOM 44 C CA . ALA A 1 7 ? -3.592 1.841 2.462 1.00 98.20 7 A 1 ATOM 45 C C . ALA A 1 7 ? -2.786 2.155 1.203 1.00 98.40 7 A 1 ATOM 46 O O . ALA A 1 7 ? -3.327 2.167 0.095 1.00 98.18 7 A 1 ATOM 47 C CB . ALA A 1 7 ? -3.888 3.121 3.235 1.00 98.04 7 A 1 ATOM 48 N N . ALA A 1 8 ? -1.491 2.388 1.374 1.00 98.14 8 A 1 ATOM 49 C CA . ALA A 1 8 ? -0.609 2.680 0.249 1.00 98.19 8 A 1 ATOM 50 C C . ALA A 1 8 ? -0.494 1.478 -0.684 1.00 98.33 8 A 1 ATOM 51 O O . ALA A 1 8 ? -0.602 1.617 -1.905 1.00 98.05 8 A 1 ATOM 52 C CB . ALA A 1 8 ? 0.766 3.087 0.767 1.00 98.00 8 A 1 ATOM 53 N N . CYS A 1 9 ? -0.295 0.285 -0.101 1.00 97.48 9 A 1 ATOM 54 C CA . CYS A 1 9 ? -0.171 -0.937 -0.885 1.00 97.60 9 A 1 ATOM 55 C C . CYS A 1 9 ? -1.461 -1.242 -1.637 1.00 97.87 9 A 1 ATOM 56 O O . CYS A 1 9 ? -1.429 -1.667 -2.788 1.00 97.16 9 A 1 ATOM 57 C CB . CYS A 1 9 ? 0.203 -2.109 0.022 1.00 97.06 9 A 1 ATOM 58 S SG . CYS A 1 9 ? 1.887 -1.970 0.665 1.00 94.22 9 A 1 ATOM 59 N N . THR A 1 10 ? -2.583 -1.012 -0.969 1.00 97.54 10 A 1 ATOM 60 C CA . THR A 1 10 ? -3.890 -1.251 -1.582 1.00 97.65 10 A 1 ATOM 61 C C . THR A 1 10 ? -4.077 -0.362 -2.807 1.00 98.10 10 A 1 ATOM 62 O O . THR A 1 10 ? -4.585 -0.812 -3.840 1.00 97.75 10 A 1 ATOM 63 C CB . THR A 1 10 ? -5.020 -0.985 -0.583 1.00 97.21 10 A 1 ATOM 64 O OG1 . THR A 1 10 ? -4.878 -1.850 0.538 1.00 94.81 10 A 1 ATOM 65 C CG2 . THR A 1 10 ? -6.381 -1.240 -1.222 1.00 94.14 10 A 1 ATOM 66 N N . LEU A 1 11 ? -3.656 0.882 -2.696 1.00 97.56 11 A 1 ATOM 67 C CA . LEU A 1 11 ? -3.751 1.821 -3.811 1.00 97.63 11 A 1 ATOM 68 C C . LEU A 1 11 ? -2.903 1.352 -4.988 1.00 98.07 11 A 1 ATOM 69 O O . LEU A 1 11 ? -3.339 1.395 -6.141 1.00 97.77 11 A 1 ATOM 70 C CB . LEU A 1 11 ? -3.301 3.212 -3.358 1.00 97.43 11 A 1 ATOM 71 C CG . LEU A 1 11 ? -3.451 4.295 -4.425 1.00 94.86 11 A 1 ATOM 72 C CD1 . LEU A 1 11 ? -4.917 4.513 -4.777 1.00 93.10 11 A 1 ATOM 73 C CD2 . LEU A 1 11 ? -2.832 5.601 -3.938 1.00 93.20 11 A 1 ATOM 74 N N . VAL A 1 12 ? -1.686 0.892 -4.687 1.00 98.12 12 A 1 ATOM 75 C CA . VAL A 1 12 ? -0.778 0.388 -5.718 1.00 98.11 12 A 1 ATOM 76 C C . VAL A 1 12 ? -1.368 -0.848 -6.388 1.00 98.33 12 A 1 ATOM 77 O O . VAL A 1 12 ? -1.340 -0.977 -7.619 1.00 98.14 12 A 1 ATOM 78 C CB . VAL A 1 12 ? 0.604 0.067 -5.129 1.00 97.73 12 A 1 ATOM 79 C CG1 . VAL A 1 12 ? 1.513 -0.571 -6.173 1.00 96.54 12 A 1 ATOM 80 C CG2 . VAL A 1 12 ? 1.252 1.337 -4.596 1.00 96.53 12 A 1 ATOM 81 N N . LEU A 1 13 ? -1.912 -1.752 -5.580 1.00 97.93 13 A 1 ATOM 82 C CA . LEU A 1 13 ? -2.512 -2.976 -6.098 1.00 97.89 13 A 1 ATOM 83 C C . LEU A 1 13 ? -3.727 -2.662 -6.964 1.00 98.28 13 A 1 ATOM 84 O O . LEU A 1 13 ? -3.944 -3.300 -7.998 1.00 98.07 13 A 1 ATOM 85 C CB . LEU A 1 13 ? -2.919 -3.890 -4.938 1.00 97.49 13 A 1 ATOM 86 C CG . LEU A 1 13 ? -1.736 -4.518 -4.199 1.00 94.02 13 A 1 ATOM 87 C CD1 . LEU A 1 13 ? -2.214 -5.193 -2.916 1.00 92.31 13 A 1 ATOM 88 C CD2 . LEU A 1 13 ? -1.018 -5.528 -5.083 1.00 91.87 13 A 1 ATOM 89 N N . ALA A 1 14 ? -4.508 -1.687 -6.543 1.00 98.05 14 A 1 ATOM 90 C CA . ALA A 1 14 ? -5.687 -1.278 -7.299 1.00 97.95 14 A 1 ATOM 91 C C . ALA A 1 14 ? -5.294 -0.685 -8.647 1.00 98.19 14 A 1 ATOM 92 O O . ALA A 1 14 ? -6.005 -0.853 -9.642 1.00 97.74 14 A 1 ATOM 93 C CB . ALA A 1 14 ? -6.496 -0.266 -6.493 1.00 97.40 14 A 1 ATOM 94 N N . ALA A 1 15 ? -4.163 0.012 -8.678 1.00 97.53 15 A 1 ATOM 95 C CA . ALA A 1 15 ? -3.657 0.617 -9.909 1.00 97.26 15 A 1 ATOM 96 C C . ALA A 1 15 ? -3.055 -0.426 -10.847 1.00 97.57 15 A 1 ATOM 97 O O . ALA A 1 15 ? -3.006 -0.222 -12.063 1.00 96.81 15 A 1 ATOM 98 C CB . ALA A 1 15 ? -2.617 1.685 -9.574 1.00 96.53 15 A 1 ATOM 99 N N . ALA A 1 16 ? -2.591 -1.550 -10.283 1.00 95.45 16 A 1 ATOM 100 C CA . ALA A 1 16 ? -1.968 -2.614 -11.054 1.00 93.92 16 A 1 ATOM 101 C C . ALA A 1 16 ? -3.007 -3.439 -11.815 1.00 93.12 16 A 1 ATOM 102 O O . ALA A 1 16 ? -4.162 -3.535 -11.371 1.00 89.66 16 A 1 ATOM 103 C CB . ALA A 1 16 ? -1.129 -3.506 -10.141 1.00 90.98 16 A 1 ATOM 104 O OXT . ALA A 1 16 ? -2.658 -4.007 -12.861 1.00 84.25 16 A 1 #