# 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_spkb23806 # _entry.id spkb23806 # 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 H15 N4 O2" 175.209 ARG y ARGININE C(C[C@@H](C(=O)O)N)CNC(=[NH2+])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 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" "C5 H11 N O2 S" 149.211 MET y METHIONINE CSCC[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" "C9 H11 N O3" 181.189 TYR y TYROSINE c1cc(ccc1C[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 ARG 2 1 n ALA 3 1 n VAL 4 1 n TYR 5 1 n ALA 6 1 n ILE 7 1 n LEU 8 1 n ALA 9 1 n GLY 10 1 n LEU 11 1 n LEU 12 1 n ALA 13 1 n THR 14 1 n GLY 15 1 n SER 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 @ 2025-07-02 20:47:53)" _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 93.08 _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 88.35 1 1 A ARG 2 2 87.43 1 2 A ALA 3 2 97.91 1 3 A VAL 4 2 97.25 1 4 A TYR 5 2 93.57 1 5 A ALA 6 2 97.79 1 6 A ILE 7 2 95.62 1 7 A LEU 8 2 94.38 1 8 A ALA 9 2 96.88 1 9 A GLY 10 2 97.61 1 10 A LEU 11 2 95.95 1 11 A LEU 12 2 95.45 1 12 A ALA 13 2 97.31 1 13 A THR 14 2 93.22 1 14 A GLY 15 2 92.34 1 15 A SER 16 2 85.31 1 16 A ALA 17 2 82.28 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 ARG . 2 A 2 A 3 1 n ALA . 3 A 3 A 4 1 n VAL . 4 A 4 A 5 1 n TYR . 5 A 5 A 6 1 n ALA . 6 A 6 A 7 1 n ILE . 7 A 7 A 8 1 n LEU . 8 A 8 A 9 1 n ALA . 9 A 9 A 10 1 n GLY . 10 A 10 A 11 1 n LEU . 11 A 11 A 12 1 n LEU . 12 A 12 A 13 1 n ALA . 13 A 13 A 14 1 n THR . 14 A 14 A 15 1 n GLY . 15 A 15 A 16 1 n SER . 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 ? -8.266 1.237 10.462 1.00 93.59 1 A 1 ATOM 2 C CA . MET A 1 1 ? -7.977 0.144 9.506 1.00 94.12 1 A 1 ATOM 3 C C . MET A 1 1 ? -6.484 0.119 9.155 1.00 94.83 1 A 1 ATOM 4 O O . MET A 1 1 ? -5.963 1.074 8.589 1.00 92.15 1 A 1 ATOM 5 C CB . MET A 1 1 ? -8.788 0.355 8.235 1.00 90.08 1 A 1 ATOM 6 C CG . MET A 1 1 ? -10.291 0.233 8.487 1.00 86.15 1 A 1 ATOM 7 S SD . MET A 1 1 ? -10.824 -1.468 8.417 1.00 83.46 1 A 1 ATOM 8 C CE . MET A 1 1 ? -12.568 -1.265 8.740 1.00 72.42 1 A 1 ATOM 9 N N . ARG A 1 2 ? -5.812 -0.973 9.485 1.00 94.70 2 A 1 ATOM 10 C CA . ARG A 1 2 ? -4.373 -1.125 9.210 1.00 96.37 2 A 1 ATOM 11 C C . ARG A 1 2 ? -4.124 -1.585 7.775 1.00 97.29 2 A 1 ATOM 12 O O . ARG A 1 2 ? -3.138 -1.197 7.162 1.00 96.02 2 A 1 ATOM 13 C CB . ARG A 1 2 ? -3.775 -2.130 10.196 1.00 94.25 2 A 1 ATOM 14 C CG . ARG A 1 2 ? -3.193 -1.467 11.415 1.00 88.73 2 A 1 ATOM 15 C CD . ARG A 1 2 ? -1.688 -1.712 11.485 1.00 86.64 2 A 1 ATOM 16 N NE . ARG A 1 2 ? -0.958 -0.940 10.484 1.00 81.83 2 A 1 ATOM 17 C CZ . ARG A 1 2 ? 0.341 -1.090 10.236 1.00 79.79 2 A 1 ATOM 18 N NH1 . ARG A 1 2 ? 1.057 -1.970 10.897 1.00 72.91 2 A 1 ATOM 19 N NH2 . ARG A 1 2 ? 0.916 -0.355 9.298 1.00 73.16 2 A 1 ATOM 20 N N . ALA A 1 3 ? -5.035 -2.406 7.241 1.00 97.56 3 A 1 ATOM 21 C CA . ALA A 1 3 ? -4.907 -2.920 5.876 1.00 98.12 3 A 1 ATOM 22 C C . ALA A 1 3 ? -4.882 -1.780 4.856 1.00 98.35 3 A 1 ATOM 23 O O . ALA A 1 3 ? -4.107 -1.806 3.900 1.00 97.81 3 A 1 ATOM 24 C CB . ALA A 1 3 ? -6.055 -3.878 5.582 1.00 97.73 3 A 1 ATOM 25 N N . VAL A 1 4 ? -5.725 -0.775 5.058 1.00 98.25 4 A 1 ATOM 26 C CA . VAL A 1 4 ? -5.789 0.384 4.159 1.00 98.26 4 A 1 ATOM 27 C C . VAL A 1 4 ? -4.458 1.135 4.163 1.00 98.32 4 A 1 ATOM 28 O O . VAL A 1 4 ? -3.965 1.554 3.116 1.00 97.94 4 A 1 ATOM 29 C CB . VAL A 1 4 ? -6.927 1.330 4.572 1.00 97.82 4 A 1 ATOM 30 C CG1 . VAL A 1 4 ? -7.029 2.495 3.601 1.00 95.25 4 A 1 ATOM 31 C CG2 . VAL A 1 4 ? -8.247 0.576 4.626 1.00 94.90 4 A 1 ATOM 32 N N . TYR A 1 5 ? -3.881 1.289 5.337 1.00 97.21 5 A 1 ATOM 33 C CA . TYR A 1 5 ? -2.599 1.986 5.461 1.00 97.08 5 A 1 ATOM 34 C C . TYR A 1 5 ? -1.484 1.194 4.782 1.00 97.27 5 A 1 ATOM 35 O O . TYR A 1 5 ? -0.548 1.772 4.230 1.00 97.19 5 A 1 ATOM 36 C CB . TYR A 1 5 ? -2.270 2.191 6.938 1.00 96.64 5 A 1 ATOM 37 C CG . TYR A 1 5 ? -2.863 3.479 7.469 1.00 93.77 5 A 1 ATOM 38 C CD1 . TYR A 1 5 ? -2.301 4.707 7.124 1.00 91.20 5 A 1 ATOM 39 C CD2 . TYR A 1 5 ? -3.974 3.458 8.303 1.00 91.60 5 A 1 ATOM 40 C CE1 . TYR A 1 5 ? -2.843 5.894 7.605 1.00 90.97 5 A 1 ATOM 41 C CE2 . TYR A 1 5 ? -4.523 4.640 8.787 1.00 90.35 5 A 1 ATOM 42 C CZ . TYR A 1 5 ? -3.952 5.857 8.436 1.00 90.74 5 A 1 ATOM 43 O OH . TYR A 1 5 ? -4.483 7.027 8.911 1.00 88.79 5 A 1 ATOM 44 N N . ALA A 1 6 ? -1.588 -0.125 4.796 1.00 97.78 6 A 1 ATOM 45 C CA . ALA A 1 6 ? -0.592 -0.989 4.160 1.00 97.85 6 A 1 ATOM 46 C C . ALA A 1 6 ? -0.552 -0.739 2.652 1.00 98.03 6 A 1 ATOM 47 O O . ALA A 1 6 ? 0.516 -0.750 2.038 1.00 97.75 6 A 1 ATOM 48 C CB . ALA A 1 6 ? -0.929 -2.447 4.440 1.00 97.56 6 A 1 ATOM 49 N N . ILE A 1 7 ? -1.715 -0.510 2.064 1.00 97.18 7 A 1 ATOM 50 C CA . ILE A 1 7 ? -1.812 -0.237 0.629 1.00 96.95 7 A 1 ATOM 51 C C . ILE A 1 7 ? -1.130 1.092 0.304 1.00 97.20 7 A 1 ATOM 52 O O . ILE A 1 7 ? -0.403 1.207 -0.689 1.00 96.80 7 A 1 ATOM 53 C CB . ILE A 1 7 ? -3.289 -0.208 0.192 1.00 96.83 7 A 1 ATOM 54 C CG1 . ILE A 1 7 ? -3.933 -1.581 0.411 1.00 95.50 7 A 1 ATOM 55 C CG2 . ILE A 1 7 ? -3.398 0.196 -1.284 1.00 94.68 7 A 1 ATOM 56 C CD1 . ILE A 1 7 ? -5.448 -1.526 0.399 1.00 89.79 7 A 1 ATOM 57 N N . LEU A 1 8 ? -1.361 2.081 1.133 1.00 96.64 8 A 1 ATOM 58 C CA . LEU A 1 8 ? -0.755 3.402 0.945 1.00 96.39 8 A 1 ATOM 59 C C . LEU A 1 8 ? 0.766 3.299 1.018 1.00 96.89 8 A 1 ATOM 60 O O . LEU A 1 8 ? 1.485 3.931 0.246 1.00 97.04 8 A 1 ATOM 61 C CB . LEU A 1 8 ? -1.276 4.374 2.017 1.00 95.82 8 A 1 ATOM 62 C CG . LEU A 1 8 ? -2.310 5.380 1.519 1.00 91.03 8 A 1 ATOM 63 C CD1 . LEU A 1 8 ? -1.701 6.287 0.457 1.00 90.80 8 A 1 ATOM 64 C CD2 . LEU A 1 8 ? -3.522 4.659 0.963 1.00 90.41 8 A 1 ATOM 65 N N . ALA A 1 9 ? 1.249 2.496 1.944 1.00 96.88 9 A 1 ATOM 66 C CA . ALA A 1 9 ? 2.687 2.294 2.119 1.00 96.90 9 A 1 ATOM 67 C C . ALA A 1 9 ? 3.293 1.638 0.881 1.00 97.32 9 A 1 ATOM 68 O O . ALA A 1 9 ? 4.418 1.951 0.496 1.00 96.97 9 A 1 ATOM 69 C CB . ALA A 1 9 ? 2.930 1.425 3.345 1.00 96.33 9 A 1 ATOM 70 N N . GLY A 1 10 ? 2.547 0.732 0.266 1.00 97.46 10 A 1 ATOM 71 C CA . GLY A 1 10 ? 3.019 0.054 -0.939 1.00 97.43 10 A 1 ATOM 72 C C . GLY A 1 10 ? 3.228 1.019 -2.087 1.00 97.90 10 A 1 ATOM 73 O O . GLY A 1 10 ? 4.226 0.940 -2.803 1.00 97.65 10 A 1 ATOM 74 N N . LEU A 1 11 ? 2.285 1.931 -2.266 1.00 97.56 11 A 1 ATOM 75 C CA . LEU A 1 11 ? 2.370 2.928 -3.336 1.00 97.37 11 A 1 ATOM 76 C C . LEU A 1 11 ? 3.596 3.822 -3.145 1.00 97.70 11 A 1 ATOM 77 O O . LEU A 1 11 ? 4.298 4.138 -4.105 1.00 97.17 11 A 1 ATOM 78 C CB . LEU A 1 11 ? 1.101 3.787 -3.338 1.00 96.93 11 A 1 ATOM 79 C CG . LEU A 1 11 ? 0.996 4.691 -4.565 1.00 95.02 11 A 1 ATOM 80 C CD1 . LEU A 1 11 ? 0.412 3.919 -5.741 1.00 93.24 11 A 1 ATOM 81 C CD2 . LEU A 1 11 ? 0.136 5.905 -4.256 1.00 92.58 11 A 1 ATOM 82 N N . LEU A 1 12 ? 3.849 4.225 -1.925 1.00 97.68 12 A 1 ATOM 83 C CA . LEU A 1 12 ? 4.995 5.085 -1.618 1.00 97.24 12 A 1 ATOM 84 C C . LEU A 1 12 ? 6.309 4.325 -1.771 1.00 97.26 12 A 1 ATOM 85 O O . LEU A 1 12 ? 7.319 4.892 -2.189 1.00 96.27 12 A 1 ATOM 86 C CB . LEU A 1 12 ? 4.857 5.631 -0.195 1.00 96.70 12 A 1 ATOM 87 C CG . LEU A 1 12 ? 5.745 6.848 0.057 1.00 94.48 12 A 1 ATOM 88 C CD1 . LEU A 1 12 ? 4.960 7.956 0.733 1.00 92.33 12 A 1 ATOM 89 C CD2 . LEU A 1 12 ? 6.945 6.461 0.907 1.00 91.63 12 A 1 ATOM 90 N N . ALA A 1 13 ? 6.295 3.042 -1.451 1.00 97.97 13 A 1 ATOM 91 C CA . ALA A 1 13 ? 7.492 2.209 -1.551 1.00 97.65 13 A 1 ATOM 92 C C . ALA A 1 13 ? 7.855 1.933 -3.007 1.00 97.62 13 A 1 ATOM 93 O O . ALA A 1 13 ? 9.032 1.910 -3.363 1.00 96.33 13 A 1 ATOM 94 C CB . ALA A 1 13 ? 7.271 0.902 -0.805 1.00 97.00 13 A 1 ATOM 95 N N . THR A 1 14 ? 6.842 1.732 -3.856 1.00 96.88 14 A 1 ATOM 96 C CA . THR A 1 14 ? 7.071 1.444 -5.277 1.00 96.02 14 A 1 ATOM 97 C C . THR A 1 14 ? 6.548 2.570 -6.170 1.00 95.73 14 A 1 ATOM 98 O O . THR A 1 14 ? 5.626 2.390 -6.957 1.00 92.25 14 A 1 ATOM 99 C CB . THR A 1 14 ? 6.426 0.103 -5.661 1.00 94.07 14 A 1 ATOM 100 O OG1 . THR A 1 14 ? 6.698 -0.178 -7.035 1.00 88.88 14 A 1 ATOM 101 C CG2 . THR A 1 14 ? 4.922 0.101 -5.440 1.00 88.69 14 A 1 ATOM 102 N N . GLY A 1 15 ? 7.143 3.726 -6.053 1.00 94.46 15 A 1 ATOM 103 C CA . GLY A 1 15 ? 6.733 4.867 -6.860 1.00 92.59 15 A 1 ATOM 104 C C . GLY A 1 15 ? 7.314 6.176 -6.357 1.00 92.73 15 A 1 ATOM 105 O O . GLY A 1 15 ? 7.414 7.150 -7.107 1.00 89.56 15 A 1 ATOM 106 N N . SER A 1 16 ? 7.695 6.212 -5.098 1.00 90.60 16 A 1 ATOM 107 C CA . SER A 1 16 ? 8.253 7.424 -4.495 1.00 88.72 16 A 1 ATOM 108 C C . SER A 1 16 ? 9.407 7.094 -3.544 1.00 89.13 16 A 1 ATOM 109 O O . SER A 1 16 ? 9.557 7.706 -2.487 1.00 83.76 16 A 1 ATOM 110 C CB . SER A 1 16 ? 7.157 8.176 -3.742 1.00 84.56 16 A 1 ATOM 111 O OG . SER A 1 16 ? 7.388 9.569 -3.796 1.00 75.08 16 A 1 ATOM 112 N N . ALA A 1 17 ? 10.232 6.119 -3.949 1.00 89.38 17 A 1 ATOM 113 C CA . ALA A 1 17 ? 11.357 5.697 -3.121 1.00 86.65 17 A 1 ATOM 114 C C . ALA A 1 17 ? 12.686 5.965 -3.825 1.00 84.61 17 A 1 ATOM 115 O O . ALA A 1 17 ? 12.715 5.987 -5.069 1.00 78.06 17 A 1 ATOM 116 C CB . ALA A 1 17 ? 11.222 4.219 -2.770 1.00 80.45 17 A 1 ATOM 117 O OXT . ALA A 1 17 ? 13.710 6.130 -3.136 1.00 74.56 17 A 1 #