data_9A38 # _entry.id 9A38 # loop_ _atom_type.symbol C H N O S # loop_ _audit_author.name _audit_author.pdbx_ordinal "Stahl, K." 1 "Graziadei, A." 2 "Dau, T." 3 "Brock, O." 4 "Rappsilber, J." 5 # loop_ _audit_conform.dict_location _audit_conform.dict_name _audit_conform.dict_version https://mmcif.wwpdb.org/dictionaries/ascii/mmcif_ihm_ext.dic mmcif_ihm_ext.dic 1.26 http://mmcif.wwpdb.org/dictionaries/ascii/mmcif_pdbx_v50.dic mmcif_pdbx.dic 5.395 # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB-Dev PDBDEV_00000193 PDBDEV_00000193 ? PDB 9A38 pdb_00009a38 10.2210/pdb9a38/pdb # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 9A38 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2023-02-03 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2023-02-24 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # _ihm_entry_collection.id PDBDEV_G_1000001 _ihm_entry_collection.name . _ihm_entry_collection.details 'Collection of entries belonging to the publication: "Protein structure prediction with in-cell photo-crosslinking mass spectrometry and deep learning"' # _ihm_entry_collection_mapping.collection_id PDBDEV_G_1000001 _ihm_entry_collection_mapping.entry_id 9A38 # loop_ _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.type "C3 H7 N O2" 89.094 ALA . ALANINE . "L-peptide linking" "C6 H15 N4 O2 1" 175.212 ARG . ARGININE . "L-peptide linking" "C4 H8 N2 O3" 132.119 ASN . ASPARAGINE . "L-peptide linking" "C4 H7 N O4" 133.103 ASP . "ASPARTIC ACID" . "L-peptide linking" "C3 H7 N O2 S" 121.154 CYS . CYSTEINE . "L-peptide linking" "C5 H10 N2 O3" 146.146 GLN . GLUTAMINE . "L-peptide linking" "C5 H9 N O4" 147.13 GLU . "GLUTAMIC ACID" . "L-peptide linking" "C2 H5 N O2" 75.067 GLY . GLYCINE . "peptide linking" "C6 H10 N3 O2 1" 156.165 HIS . HISTIDINE . "L-peptide linking" "C6 H13 N O2" 131.175 ILE . ISOLEUCINE . "L-peptide linking" "C6 H13 N O2" 131.175 LEU . LEUCINE . "L-peptide linking" "C6 H15 N2 O2 1" 147.198 LYS . LYSINE . "L-peptide linking" "C5 H11 N O2 S" 149.208 MET . METHIONINE . "L-peptide linking" "C9 H11 N O2" 165.192 PHE . PHENYLALANINE . "L-peptide linking" "C5 H9 N O2" 115.132 PRO . PROLINE . "L-peptide linking" "C3 H7 N O3" 105.093 SER . SERINE . "L-peptide linking" "C4 H9 N O3" 119.12 THR . THREONINE . "L-peptide linking" "C11 H12 N2 O2" 204.229 TRP . TRYPTOPHAN . "L-peptide linking" "C9 H11 N O3" 181.191 TYR . TYROSINE . "L-peptide linking" "C5 H11 N O2" 117.148 VAL . VALINE . "L-peptide linking" # _citation.country . _citation.id 1 _citation.journal_abbrev "Nature Biotechnology" _citation.journal_id_ASTM . _citation.journal_id_CSD . _citation.journal_id_ISSN . _citation.journal_issue . _citation.journal_volume . _citation.page_first . _citation.page_last . _citation.pdbx_database_id_DOI 10.1038/s41587-023-01704-z _citation.pdbx_database_id_PubMed 36941363 _citation.title "Protein structure prediction with in-cell photo-crosslinking mass spectrometry and deep learning" _citation.year 2023 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal 1 "Stahl, K." 1 1 "Graziadei, A." 2 1 "Dau, T." 3 1 "Brock, O." 4 1 "Rappsilber, J." 5 # _entity.details . _entity.formula_weight 34328.027 _entity.id 1 _entity.pdbx_description P28635 _entity.pdbx_number_of_molecules 1 _entity.src_method NAT _entity.type polymer # _entity_poly.entity_id 1 _entity_poly.nstd_chirality . _entity_poly.nstd_linkage NO _entity_poly.nstd_monomer NO _entity_poly.pdbx_seq_one_letter_code MAFKFKTFAAVGALIGSLALVGCGQDEKDPNHIKVGVIVGAEQQVAEVAQKVAKDKYGLDVELVTFNDYVLPNEALSKGDIDANAFQHKPYLDQQLKDRGYKLVAVGNTFVYPIAGYSKKIKSLDELQDGSQVAVPNDPTNLGRSLLLLQKVGLIKLKDGVGLLPTVLDVVENPKNLKIVELEAPQLPRSLDDAQIALAVINTTYASQIGLTPAKDGIFVEDKESPYVNLIVTREDNKDAENVKKFVQAYQSDEVYEAANKVFNGGAVKGW _entity_poly.pdbx_seq_one_letter_code_can MAFKFKTFAAVGALIGSLALVGCGQDEKDPNHIKVGVIVGAEQQVAEVAQKVAKDKYGLDVELVTFNDYVLPNEALSKGDIDANAFQHKPYLDQQLKDRGYKLVAVGNTFVYPIAGYSKKIKSLDELQDGSQVAVPNDPTNLGRSLLLLQKVGLIKLKDGVGLLPTVLDVVENPKNLKIVELEAPQLPRSLDDAQIALAVINTTYASQIGLTPAKDGIFVEDKESPYVNLIVTREDNKDAENVKKFVQAYQSDEVYEAANKVFNGGAVKGW _entity_poly.pdbx_sequence_evidence_code . _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 . MET 1 1 . ALA 2 1 . PHE 3 1 . LYS 4 1 . PHE 5 1 . LYS 6 1 . THR 7 1 . PHE 8 1 . ALA 9 1 . ALA 10 1 . VAL 11 1 . GLY 12 1 . ALA 13 1 . LEU 14 1 . ILE 15 1 . GLY 16 1 . SER 17 1 . LEU 18 1 . ALA 19 1 . LEU 20 1 . VAL 21 1 . GLY 22 1 . CYS 23 1 . GLY 24 1 . GLN 25 1 . ASP 26 1 . GLU 27 1 . LYS 28 1 . ASP 29 1 . PRO 30 1 . ASN 31 1 . HIS 32 1 . ILE 33 1 . LYS 34 1 . VAL 35 1 . GLY 36 1 . VAL 37 1 . ILE 38 1 . VAL 39 1 . GLY 40 1 . ALA 41 1 . GLU 42 1 . GLN 43 1 . GLN 44 1 . VAL 45 1 . ALA 46 1 . GLU 47 1 . VAL 48 1 . ALA 49 1 . GLN 50 1 . LYS 51 1 . VAL 52 1 . ALA 53 1 . LYS 54 1 . ASP 55 1 . LYS 56 1 . TYR 57 1 . GLY 58 1 . LEU 59 1 . ASP 60 1 . VAL 61 1 . GLU 62 1 . LEU 63 1 . VAL 64 1 . THR 65 1 . PHE 66 1 . ASN 67 1 . ASP 68 1 . TYR 69 1 . VAL 70 1 . LEU 71 1 . PRO 72 1 . ASN 73 1 . GLU 74 1 . ALA 75 1 . LEU 76 1 . SER 77 1 . LYS 78 1 . GLY 79 1 . ASP 80 1 . ILE 81 1 . ASP 82 1 . ALA 83 1 . ASN 84 1 . ALA 85 1 . PHE 86 1 . GLN 87 1 . HIS 88 1 . LYS 89 1 . PRO 90 1 . TYR 91 1 . LEU 92 1 . ASP 93 1 . GLN 94 1 . GLN 95 1 . LEU 96 1 . LYS 97 1 . ASP 98 1 . ARG 99 1 . GLY 100 1 . TYR 101 1 . LYS 102 1 . LEU 103 1 . VAL 104 1 . ALA 105 1 . VAL 106 1 . GLY 107 1 . ASN 108 1 . THR 109 1 . PHE 110 1 . VAL 111 1 . TYR 112 1 . PRO 113 1 . ILE 114 1 . ALA 115 1 . GLY 116 1 . TYR 117 1 . SER 118 1 . LYS 119 1 . LYS 120 1 . ILE 121 1 . LYS 122 1 . SER 123 1 . LEU 124 1 . ASP 125 1 . GLU 126 1 . LEU 127 1 . GLN 128 1 . ASP 129 1 . GLY 130 1 . SER 131 1 . GLN 132 1 . VAL 133 1 . ALA 134 1 . VAL 135 1 . PRO 136 1 . ASN 137 1 . ASP 138 1 . PRO 139 1 . THR 140 1 . ASN 141 1 . LEU 142 1 . GLY 143 1 . ARG 144 1 . SER 145 1 . LEU 146 1 . LEU 147 1 . LEU 148 1 . LEU 149 1 . GLN 150 1 . LYS 151 1 . VAL 152 1 . GLY 153 1 . LEU 154 1 . ILE 155 1 . LYS 156 1 . LEU 157 1 . LYS 158 1 . ASP 159 1 . GLY 160 1 . VAL 161 1 . GLY 162 1 . LEU 163 1 . LEU 164 1 . PRO 165 1 . THR 166 1 . VAL 167 1 . LEU 168 1 . ASP 169 1 . VAL 170 1 . VAL 171 1 . GLU 172 1 . ASN 173 1 . PRO 174 1 . LYS 175 1 . ASN 176 1 . LEU 177 1 . LYS 178 1 . ILE 179 1 . VAL 180 1 . GLU 181 1 . LEU 182 1 . GLU 183 1 . ALA 184 1 . PRO 185 1 . GLN 186 1 . LEU 187 1 . PRO 188 1 . ARG 189 1 . SER 190 1 . LEU 191 1 . ASP 192 1 . ASP 193 1 . ALA 194 1 . GLN 195 1 . ILE 196 1 . ALA 197 1 . LEU 198 1 . ALA 199 1 . VAL 200 1 . ILE 201 1 . ASN 202 1 . THR 203 1 . THR 204 1 . TYR 205 1 . ALA 206 1 . SER 207 1 . GLN 208 1 . ILE 209 1 . GLY 210 1 . LEU 211 1 . THR 212 1 . PRO 213 1 . ALA 214 1 . LYS 215 1 . ASP 216 1 . GLY 217 1 . ILE 218 1 . PHE 219 1 . VAL 220 1 . GLU 221 1 . ASP 222 1 . LYS 223 1 . GLU 224 1 . SER 225 1 . PRO 226 1 . TYR 227 1 . VAL 228 1 . ASN 229 1 . LEU 230 1 . ILE 231 1 . VAL 232 1 . THR 233 1 . ARG 234 1 . GLU 235 1 . ASP 236 1 . ASN 237 1 . LYS 238 1 . ASP 239 1 . ALA 240 1 . GLU 241 1 . ASN 242 1 . VAL 243 1 . LYS 244 1 . LYS 245 1 . PHE 246 1 . VAL 247 1 . GLN 248 1 . ALA 249 1 . TYR 250 1 . GLN 251 1 . SER 252 1 . ASP 253 1 . GLU 254 1 . VAL 255 1 . TYR 256 1 . GLU 257 1 . ALA 258 1 . ALA 259 1 . ASN 260 1 . LYS 261 1 . VAL 262 1 . PHE 263 1 . ASN 264 1 . GLY 265 1 . GLY 266 1 . ALA 267 1 . VAL 268 1 . LYS 269 1 . GLY 270 1 . TRP 271 # _ihm_chemical_component_descriptor.auth_name L-Photo-Leucine _ihm_chemical_component_descriptor.chemical_name . _ihm_chemical_component_descriptor.common_name L-Photo-Leucine _ihm_chemical_component_descriptor.details . _ihm_chemical_component_descriptor.id 1 _ihm_chemical_component_descriptor.inchi 1S/C5H9N3O2/c1-5(7-8-5)2-3(6)4(9)10/h3H,2,6H2,1H3,(H,9,10)/t3-/m0/s1 _ihm_chemical_component_descriptor.inchi_key MJRDGTVDJKACQZ-VKHMYHEASA-N _ihm_chemical_component_descriptor.smiles CC1(C[C@H](N)C(O)=O)N=N1 _ihm_chemical_component_descriptor.smiles_canonical . # loop_ _ihm_cross_link_list.comp_id_1 _ihm_cross_link_list.comp_id_2 _ihm_cross_link_list.dataset_list_id _ihm_cross_link_list.details _ihm_cross_link_list.entity_description_1 _ihm_cross_link_list.entity_description_2 _ihm_cross_link_list.entity_id_1 _ihm_cross_link_list.entity_id_2 _ihm_cross_link_list.group_id _ihm_cross_link_list.id _ihm_cross_link_list.linker_chem_comp_descriptor_id _ihm_cross_link_list.linker_type _ihm_cross_link_list.seq_id_1 _ihm_cross_link_list.seq_id_2 LEU ILE 1 . P28635 P28635 1 1 1 1 1 L-Photo-Leucine 142 179 LEU GLU 1 . P28635 P28635 1 1 2 2 1 L-Photo-Leucine 142 181 LEU VAL 1 . P28635 P28635 1 1 3 3 1 L-Photo-Leucine 142 180 LEU VAL 1 . P28635 P28635 1 1 4 4 1 L-Photo-Leucine 163 220 PRO LEU 1 . P28635 P28635 1 1 5 5 1 L-Photo-Leucine 90 103 LEU TYR 1 . P28635 P28635 1 1 6 6 1 L-Photo-Leucine 147 227 LEU LEU 1 . P28635 P28635 1 1 7 7 1 L-Photo-Leucine 142 182 GLU LEU 1 . P28635 P28635 1 1 8 8 1 L-Photo-Leucine 47 63 LEU TYR 1 . P28635 P28635 1 1 9 9 1 L-Photo-Leucine 163 227 HIS LEU 1 . P28635 P28635 1 1 10 10 1 L-Photo-Leucine 88 103 LEU TYR 1 . P28635 P28635 1 1 11 11 1 L-Photo-Leucine 164 227 LEU GLU 1 . P28635 P28635 1 1 12 12 1 L-Photo-Leucine 148 221 LEU SER 1 . P28635 P28635 1 1 13 13 1 L-Photo-Leucine 147 225 ASP LEU 1 . P28635 P28635 1 1 14 14 1 L-Photo-Leucine 93 103 LYS LEU 1 . P28635 P28635 1 1 15 15 1 L-Photo-Leucine 97 103 LEU ASP 1 . P28635 P28635 1 1 16 16 1 L-Photo-Leucine 148 222 LEU GLU 1 . P28635 P28635 1 1 17 17 1 L-Photo-Leucine 148 224 LEU TYR 1 . P28635 P28635 1 1 18 18 1 L-Photo-Leucine 63 250 LEU VAL 1 . P28635 P28635 1 1 19 19 1 L-Photo-Leucine 147 228 VAL LEU 1 . P28635 P28635 1 1 20 20 1 L-Photo-Leucine 45 63 VAL LEU 1 . P28635 P28635 1 1 21 21 1 L-Photo-Leucine 135 168 GLY LEU 1 . P28635 P28635 1 1 22 22 1 L-Photo-Leucine 143 182 LEU LEU 1 . P28635 P28635 1 1 23 23 1 L-Photo-Leucine 149 163 LEU LEU 1 . P28635 P28635 1 1 24 24 1 L-Photo-Leucine 142 187 # loop_ _ihm_cross_link_restraint.asym_id_1 _ihm_cross_link_restraint.asym_id_2 _ihm_cross_link_restraint.atom_id_1 _ihm_cross_link_restraint.atom_id_2 _ihm_cross_link_restraint.comp_id_1 _ihm_cross_link_restraint.comp_id_2 _ihm_cross_link_restraint.conditional_crosslink_flag _ihm_cross_link_restraint.distance_threshold _ihm_cross_link_restraint.entity_id_1 _ihm_cross_link_restraint.entity_id_2 _ihm_cross_link_restraint.group_id _ihm_cross_link_restraint.id _ihm_cross_link_restraint.model_granularity _ihm_cross_link_restraint.pseudo_site_flag _ihm_cross_link_restraint.psi _ihm_cross_link_restraint.restraint_type _ihm_cross_link_restraint.seq_id_1 _ihm_cross_link_restraint.seq_id_2 _ihm_cross_link_restraint.sigma_1 _ihm_cross_link_restraint.sigma_2 A A . . LEU ILE . 10 1 1 1 1 by-residue NO 0.05 "upper bound" 142 179 . . A A . . LEU GLU . 10 1 1 2 2 by-residue NO 0.05 "upper bound" 142 181 . . A A . . LEU VAL . 10 1 1 3 3 by-residue NO 0.05 "upper bound" 142 180 . . A A . . LEU VAL . 10 1 1 4 4 by-residue NO 0.05 "upper bound" 163 220 . . A A . . PRO LEU . 10 1 1 5 5 by-residue NO 0.05 "upper bound" 90 103 . . A A . . LEU TYR . 10 1 1 6 6 by-residue NO 0.05 "upper bound" 147 227 . . A A . . LEU LEU . 10 1 1 7 7 by-residue NO 0.05 "upper bound" 142 182 . . A A . . GLU LEU . 10 1 1 8 8 by-residue NO 0.05 "upper bound" 47 63 . . A A . . LEU TYR . 10 1 1 9 9 by-residue NO 0.05 "upper bound" 163 227 . . A A . . HIS LEU . 10 1 1 10 10 by-residue NO 0.05 "upper bound" 88 103 . . A A . . LEU TYR . 10 1 1 11 11 by-residue NO 0.05 "upper bound" 164 227 . . A A . . LEU GLU . 10 1 1 12 12 by-residue NO 0.05 "upper bound" 148 221 . . A A . . LEU SER . 10 1 1 13 13 by-residue NO 0.05 "upper bound" 147 225 . . A A . . ASP LEU . 10 1 1 14 14 by-residue NO 0.05 "upper bound" 93 103 . . A A . . LYS LEU . 10 1 1 15 15 by-residue NO 0.05 "upper bound" 97 103 . . A A . . LEU ASP . 10 1 1 16 16 by-residue NO 0.05 "upper bound" 148 222 . . A A . . LEU GLU . 10 1 1 17 17 by-residue NO 0.05 "upper bound" 148 224 . . A A . . LEU TYR . 10 1 1 18 18 by-residue NO 0.05 "upper bound" 63 250 . . A A . . LEU VAL . 10 1 1 19 19 by-residue NO 0.05 "upper bound" 147 228 . . A A . . VAL LEU . 10 1 1 20 20 by-residue NO 0.05 "upper bound" 45 63 . . A A . . VAL LEU . 10 1 1 21 21 by-residue NO 0.05 "upper bound" 135 168 . . A A . . GLY LEU . 10 1 1 22 22 by-residue NO 0.05 "upper bound" 143 182 . . A A . . LEU LEU . 10 1 1 23 23 by-residue NO 0.05 "upper bound" 149 163 . . A A . . LEU LEU . 10 1 1 24 24 by-residue NO 0.05 "upper bound" 142 187 . . # _ihm_dataset_group.application . _ihm_dataset_group.details . _ihm_dataset_group.id 1 _ihm_dataset_group.name . # _ihm_dataset_group_link.dataset_list_id 1 _ihm_dataset_group_link.group_id 1 # _ihm_dataset_list.data_type "Crosslinking-MS data" _ihm_dataset_list.database_hosted YES _ihm_dataset_list.details . _ihm_dataset_list.id 1 # _ihm_dataset_related_db_reference.accession_code JPST001851 _ihm_dataset_related_db_reference.dataset_list_id 1 _ihm_dataset_related_db_reference.db_name jPOSTrepo _ihm_dataset_related_db_reference.details . _ihm_dataset_related_db_reference.id 1 _ihm_dataset_related_db_reference.version . # _ihm_entity_poly_segment.comp_id_begin MET _ihm_entity_poly_segment.comp_id_end TRP _ihm_entity_poly_segment.entity_id 1 _ihm_entity_poly_segment.id 1 _ihm_entity_poly_segment.seq_id_begin 1 _ihm_entity_poly_segment.seq_id_end 271 # _ihm_model_group.details . _ihm_model_group.id 1 _ihm_model_group.name . # loop_ _ihm_model_group_link.group_id _ihm_model_group_link.model_id 1 1 1 2 1 3 1 4 1 5 1 6 1 7 1 8 1 9 1 10 # loop_ _ihm_model_list.assembly_id _ihm_model_list.model_id _ihm_model_list.model_name _ihm_model_list.protocol_id _ihm_model_list.representation_id 1 1 . 1 1 1 2 . 1 1 1 3 . 1 1 1 4 . 1 1 1 5 . 1 1 1 6 . 1 1 1 7 . 1 1 1 8 . 1 1 1 9 . 1 1 1 10 . 1 1 # _ihm_model_representation.details . _ihm_model_representation.id 1 _ihm_model_representation.name . # _ihm_model_representation_details.description . _ihm_model_representation_details.entity_asym_id A _ihm_model_representation_details.entity_description P28635 _ihm_model_representation_details.entity_id 1 _ihm_model_representation_details.entity_poly_segment_id 1 _ihm_model_representation_details.id 1 _ihm_model_representation_details.model_granularity by-atom _ihm_model_representation_details.model_mode flexible _ihm_model_representation_details.model_object_count . _ihm_model_representation_details.model_object_primitive atomistic _ihm_model_representation_details.representation_id 1 _ihm_model_representation_details.starting_model_id . # _ihm_modeling_protocol.details . _ihm_modeling_protocol.id 1 _ihm_modeling_protocol.num_steps 1 _ihm_modeling_protocol.protocol_name AlphaLink # _ihm_modeling_protocol_details.dataset_group_id 1 _ihm_modeling_protocol_details.description . _ihm_modeling_protocol_details.ensemble_flag YES _ihm_modeling_protocol_details.id 1 _ihm_modeling_protocol_details.multi_scale_flag NO _ihm_modeling_protocol_details.multi_state_flag NO _ihm_modeling_protocol_details.num_models_begin 0 _ihm_modeling_protocol_details.num_models_end 10 _ihm_modeling_protocol_details.ordered_flag NO _ihm_modeling_protocol_details.protocol_id 1 _ihm_modeling_protocol_details.script_file_id . _ihm_modeling_protocol_details.software_id . _ihm_modeling_protocol_details.step_id 1 _ihm_modeling_protocol_details.step_method "AlphaLink with 10 msa subsamples" _ihm_modeling_protocol_details.step_name AlphaLink _ihm_modeling_protocol_details.struct_assembly_description . _ihm_modeling_protocol_details.struct_assembly_id 1 # _ihm_struct_assembly.description "Integrative modeling using in-cell photo-crosslinking mass spectrometry and deep learning" _ihm_struct_assembly.id 1 _ihm_struct_assembly.name "Integrative model" # _ihm_struct_assembly_details.assembly_id 1 _ihm_struct_assembly_details.asym_id A _ihm_struct_assembly_details.entity_description P28635 _ihm_struct_assembly_details.entity_id 1 _ihm_struct_assembly_details.entity_poly_segment_id 1 _ihm_struct_assembly_details.id 1 _ihm_struct_assembly_details.parent_assembly_id 1 # _software.citation_id 1 _software.classification "model building" _software.description "protein structure prediction by deep learning assisted by experimental distance restraints" _software.location https://github.com/lhatsk/AlphaLink _software.name AlphaLink _software.pdbx_ordinal 1 _software.type program _software.version 1.0 # _struct.entry_id 9A38 _struct.pdbx_CASP_flag . _struct.pdbx_descriptor . _struct.pdbx_details . _struct.pdbx_model_details . _struct.pdbx_model_type_details . _struct.title "Model of E. coli MetQ by in-cell photo-crosslinking MS and deep learning" _struct.pdbx_structure_determination_methodology integrative # _struct_asym.details P28635 _struct_asym.entity_id 1 _struct_asym.id A _struct_asym.pdbx_PDB_id . _struct_asym.pdbx_alt_id . _struct_asym.pdbx_blank_PDB_chainid_flag . _struct_asym.pdbx_modified . _struct_asym.pdbx_order . _struct_asym.pdbx_type . # _struct_ref.db_code METQ_ECOLI _struct_ref.db_name UNP _struct_ref.details "D-methionine-binding lipoprotein MetQ OS=Escherichia coli (strain K12) OX=83333 GN=metQ PE=1 SV=2" _struct_ref.entity_id 1 _struct_ref.id 1 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_accession P28635 _struct_ref.pdbx_seq_one_letter_code MAFKFKTFAAVGALIGSLALVGCGQDEKDPNHIKVGVIVGAEQQVAEVAQKVAKDKYGLDVELVTFNDYVLPNEALSKGDIDANAFQHKPYLDQQLKDRGYKLVAVGNTFVYPIAGYSKKIKSLDELQDGSQVAVPNDPTNLGRSLLLLQKVGLIKLKDGVGLLPTVLDVVENPKNLKIVELEAPQLPRSLDDAQIALAVINTTYASQIGLTPAKDGIFVEDKESPYVNLIVTREDNKDAENVKKFVQAYQSDEVYEAANKVFNGGAVKGW # _struct_ref_seq.align_id 1 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.db_align_end 271 _struct_ref_seq.ref_id 1 _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.seq_align_end 271 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code A 1 1 MET 1 1 MET MET A . A 1 2 ALA 2 2 ALA ALA A . A 1 3 PHE 3 3 PHE PHE A . A 1 4 LYS 4 4 LYS LYS A . A 1 5 PHE 5 5 PHE PHE A . A 1 6 LYS 6 6 LYS LYS A . A 1 7 THR 7 7 THR THR A . A 1 8 PHE 8 8 PHE PHE A . A 1 9 ALA 9 9 ALA ALA A . A 1 10 ALA 10 10 ALA ALA A . A 1 11 VAL 11 11 VAL VAL A . A 1 12 GLY 12 12 GLY GLY A . A 1 13 ALA 13 13 ALA ALA A . A 1 14 LEU 14 14 LEU LEU A . A 1 15 ILE 15 15 ILE ILE A . A 1 16 GLY 16 16 GLY GLY A . A 1 17 SER 17 17 SER SER A . A 1 18 LEU 18 18 LEU LEU A . A 1 19 ALA 19 19 ALA ALA A . A 1 20 LEU 20 20 LEU LEU A . A 1 21 VAL 21 21 VAL VAL A . A 1 22 GLY 22 22 GLY GLY A . A 1 23 CYS 23 23 CYS CYS A . A 1 24 GLY 24 24 GLY GLY A . A 1 25 GLN 25 25 GLN GLN A . A 1 26 ASP 26 26 ASP ASP A . A 1 27 GLU 27 27 GLU GLU A . A 1 28 LYS 28 28 LYS LYS A . A 1 29 ASP 29 29 ASP ASP A . A 1 30 PRO 30 30 PRO PRO A . A 1 31 ASN 31 31 ASN ASN A . A 1 32 HIS 32 32 HIS HIS A . A 1 33 ILE 33 33 ILE ILE A . A 1 34 LYS 34 34 LYS LYS A . A 1 35 VAL 35 35 VAL VAL A . A 1 36 GLY 36 36 GLY GLY A . A 1 37 VAL 37 37 VAL VAL A . A 1 38 ILE 38 38 ILE ILE A . A 1 39 VAL 39 39 VAL VAL A . A 1 40 GLY 40 40 GLY GLY A . A 1 41 ALA 41 41 ALA ALA A . A 1 42 GLU 42 42 GLU GLU A . A 1 43 GLN 43 43 GLN GLN A . A 1 44 GLN 44 44 GLN GLN A . A 1 45 VAL 45 45 VAL VAL A . A 1 46 ALA 46 46 ALA ALA A . A 1 47 GLU 47 47 GLU GLU A . A 1 48 VAL 48 48 VAL VAL A . A 1 49 ALA 49 49 ALA ALA A . A 1 50 GLN 50 50 GLN GLN A . A 1 51 LYS 51 51 LYS LYS A . A 1 52 VAL 52 52 VAL VAL A . A 1 53 ALA 53 53 ALA ALA A . A 1 54 LYS 54 54 LYS LYS A . A 1 55 ASP 55 55 ASP ASP A . A 1 56 LYS 56 56 LYS LYS A . A 1 57 TYR 57 57 TYR TYR A . A 1 58 GLY 58 58 GLY GLY A . A 1 59 LEU 59 59 LEU LEU A . A 1 60 ASP 60 60 ASP ASP A . A 1 61 VAL 61 61 VAL VAL A . A 1 62 GLU 62 62 GLU GLU A . A 1 63 LEU 63 63 LEU LEU A . A 1 64 VAL 64 64 VAL VAL A . A 1 65 THR 65 65 THR THR A . A 1 66 PHE 66 66 PHE PHE A . A 1 67 ASN 67 67 ASN ASN A . A 1 68 ASP 68 68 ASP ASP A . A 1 69 TYR 69 69 TYR TYR A . A 1 70 VAL 70 70 VAL VAL A . A 1 71 LEU 71 71 LEU LEU A . A 1 72 PRO 72 72 PRO PRO A . A 1 73 ASN 73 73 ASN ASN A . A 1 74 GLU 74 74 GLU GLU A . A 1 75 ALA 75 75 ALA ALA A . A 1 76 LEU 76 76 LEU LEU A . A 1 77 SER 77 77 SER SER A . A 1 78 LYS 78 78 LYS LYS A . A 1 79 GLY 79 79 GLY GLY A . A 1 80 ASP 80 80 ASP ASP A . A 1 81 ILE 81 81 ILE ILE A . A 1 82 ASP 82 82 ASP ASP A . A 1 83 ALA 83 83 ALA ALA A . A 1 84 ASN 84 84 ASN ASN A . A 1 85 ALA 85 85 ALA ALA A . A 1 86 PHE 86 86 PHE PHE A . A 1 87 GLN 87 87 GLN GLN A . A 1 88 HIS 88 88 HIS HIS A . A 1 89 LYS 89 89 LYS LYS A . A 1 90 PRO 90 90 PRO PRO A . A 1 91 TYR 91 91 TYR TYR A . A 1 92 LEU 92 92 LEU LEU A . A 1 93 ASP 93 93 ASP ASP A . A 1 94 GLN 94 94 GLN GLN A . A 1 95 GLN 95 95 GLN GLN A . A 1 96 LEU 96 96 LEU LEU A . A 1 97 LYS 97 97 LYS LYS A . A 1 98 ASP 98 98 ASP ASP A . A 1 99 ARG 99 99 ARG ARG A . A 1 100 GLY 100 100 GLY GLY A . A 1 101 TYR 101 101 TYR TYR A . A 1 102 LYS 102 102 LYS LYS A . A 1 103 LEU 103 103 LEU LEU A . A 1 104 VAL 104 104 VAL VAL A . A 1 105 ALA 105 105 ALA ALA A . A 1 106 VAL 106 106 VAL VAL A . A 1 107 GLY 107 107 GLY GLY A . A 1 108 ASN 108 108 ASN ASN A . A 1 109 THR 109 109 THR THR A . A 1 110 PHE 110 110 PHE PHE A . A 1 111 VAL 111 111 VAL VAL A . A 1 112 TYR 112 112 TYR TYR A . A 1 113 PRO 113 113 PRO PRO A . A 1 114 ILE 114 114 ILE ILE A . A 1 115 ALA 115 115 ALA ALA A . A 1 116 GLY 116 116 GLY GLY A . A 1 117 TYR 117 117 TYR TYR A . A 1 118 SER 118 118 SER SER A . A 1 119 LYS 119 119 LYS LYS A . A 1 120 LYS 120 120 LYS LYS A . A 1 121 ILE 121 121 ILE ILE A . A 1 122 LYS 122 122 LYS LYS A . A 1 123 SER 123 123 SER SER A . A 1 124 LEU 124 124 LEU LEU A . A 1 125 ASP 125 125 ASP ASP A . A 1 126 GLU 126 126 GLU GLU A . A 1 127 LEU 127 127 LEU LEU A . A 1 128 GLN 128 128 GLN GLN A . A 1 129 ASP 129 129 ASP ASP A . A 1 130 GLY 130 130 GLY GLY A . A 1 131 SER 131 131 SER SER A . A 1 132 GLN 132 132 GLN GLN A . A 1 133 VAL 133 133 VAL VAL A . A 1 134 ALA 134 134 ALA ALA A . A 1 135 VAL 135 135 VAL VAL A . A 1 136 PRO 136 136 PRO PRO A . A 1 137 ASN 137 137 ASN ASN A . A 1 138 ASP 138 138 ASP ASP A . A 1 139 PRO 139 139 PRO PRO A . A 1 140 THR 140 140 THR THR A . A 1 141 ASN 141 141 ASN ASN A . A 1 142 LEU 142 142 LEU LEU A . A 1 143 GLY 143 143 GLY GLY A . A 1 144 ARG 144 144 ARG ARG A . A 1 145 SER 145 145 SER SER A . A 1 146 LEU 146 146 LEU LEU A . A 1 147 LEU 147 147 LEU LEU A . A 1 148 LEU 148 148 LEU LEU A . A 1 149 LEU 149 149 LEU LEU A . A 1 150 GLN 150 150 GLN GLN A . A 1 151 LYS 151 151 LYS LYS A . A 1 152 VAL 152 152 VAL VAL A . A 1 153 GLY 153 153 GLY GLY A . A 1 154 LEU 154 154 LEU LEU A . A 1 155 ILE 155 155 ILE ILE A . A 1 156 LYS 156 156 LYS LYS A . A 1 157 LEU 157 157 LEU LEU A . A 1 158 LYS 158 158 LYS LYS A . A 1 159 ASP 159 159 ASP ASP A . A 1 160 GLY 160 160 GLY GLY A . A 1 161 VAL 161 161 VAL VAL A . A 1 162 GLY 162 162 GLY GLY A . A 1 163 LEU 163 163 LEU LEU A . A 1 164 LEU 164 164 LEU LEU A . A 1 165 PRO 165 165 PRO PRO A . A 1 166 THR 166 166 THR THR A . A 1 167 VAL 167 167 VAL VAL A . A 1 168 LEU 168 168 LEU LEU A . A 1 169 ASP 169 169 ASP ASP A . A 1 170 VAL 170 170 VAL VAL A . A 1 171 VAL 171 171 VAL VAL A . A 1 172 GLU 172 172 GLU GLU A . A 1 173 ASN 173 173 ASN ASN A . A 1 174 PRO 174 174 PRO PRO A . A 1 175 LYS 175 175 LYS LYS A . A 1 176 ASN 176 176 ASN ASN A . A 1 177 LEU 177 177 LEU LEU A . A 1 178 LYS 178 178 LYS LYS A . A 1 179 ILE 179 179 ILE ILE A . A 1 180 VAL 180 180 VAL VAL A . A 1 181 GLU 181 181 GLU GLU A . A 1 182 LEU 182 182 LEU LEU A . A 1 183 GLU 183 183 GLU GLU A . A 1 184 ALA 184 184 ALA ALA A . A 1 185 PRO 185 185 PRO PRO A . A 1 186 GLN 186 186 GLN GLN A . A 1 187 LEU 187 187 LEU LEU A . A 1 188 PRO 188 188 PRO PRO A . A 1 189 ARG 189 189 ARG ARG A . A 1 190 SER 190 190 SER SER A . A 1 191 LEU 191 191 LEU LEU A . A 1 192 ASP 192 192 ASP ASP A . A 1 193 ASP 193 193 ASP ASP A . A 1 194 ALA 194 194 ALA ALA A . A 1 195 GLN 195 195 GLN GLN A . A 1 196 ILE 196 196 ILE ILE A . A 1 197 ALA 197 197 ALA ALA A . A 1 198 LEU 198 198 LEU LEU A . A 1 199 ALA 199 199 ALA ALA A . A 1 200 VAL 200 200 VAL VAL A . A 1 201 ILE 201 201 ILE ILE A . A 1 202 ASN 202 202 ASN ASN A . A 1 203 THR 203 203 THR THR A . A 1 204 THR 204 204 THR THR A . A 1 205 TYR 205 205 TYR TYR A . A 1 206 ALA 206 206 ALA ALA A . A 1 207 SER 207 207 SER SER A . A 1 208 GLN 208 208 GLN GLN A . A 1 209 ILE 209 209 ILE ILE A . A 1 210 GLY 210 210 GLY GLY A . A 1 211 LEU 211 211 LEU LEU A . A 1 212 THR 212 212 THR THR A . A 1 213 PRO 213 213 PRO PRO A . A 1 214 ALA 214 214 ALA ALA A . A 1 215 LYS 215 215 LYS LYS A . A 1 216 ASP 216 216 ASP ASP A . A 1 217 GLY 217 217 GLY GLY A . A 1 218 ILE 218 218 ILE ILE A . A 1 219 PHE 219 219 PHE PHE A . A 1 220 VAL 220 220 VAL VAL A . A 1 221 GLU 221 221 GLU GLU A . A 1 222 ASP 222 222 ASP ASP A . A 1 223 LYS 223 223 LYS LYS A . A 1 224 GLU 224 224 GLU GLU A . A 1 225 SER 225 225 SER SER A . A 1 226 PRO 226 226 PRO PRO A . A 1 227 TYR 227 227 TYR TYR A . A 1 228 VAL 228 228 VAL VAL A . A 1 229 ASN 229 229 ASN ASN A . A 1 230 LEU 230 230 LEU LEU A . A 1 231 ILE 231 231 ILE ILE A . A 1 232 VAL 232 232 VAL VAL A . A 1 233 THR 233 233 THR THR A . A 1 234 ARG 234 234 ARG ARG A . A 1 235 GLU 235 235 GLU GLU A . A 1 236 ASP 236 236 ASP ASP A . A 1 237 ASN 237 237 ASN ASN A . A 1 238 LYS 238 238 LYS LYS A . A 1 239 ASP 239 239 ASP ASP A . A 1 240 ALA 240 240 ALA ALA A . A 1 241 GLU 241 241 GLU GLU A . A 1 242 ASN 242 242 ASN ASN A . A 1 243 VAL 243 243 VAL VAL A . A 1 244 LYS 244 244 LYS LYS A . A 1 245 LYS 245 245 LYS LYS A . A 1 246 PHE 246 246 PHE PHE A . A 1 247 VAL 247 247 VAL VAL A . A 1 248 GLN 248 248 GLN GLN A . A 1 249 ALA 249 249 ALA ALA A . A 1 250 TYR 250 250 TYR TYR A . A 1 251 GLN 251 251 GLN GLN A . A 1 252 SER 252 252 SER SER A . A 1 253 ASP 253 253 ASP ASP A . A 1 254 GLU 254 254 GLU GLU A . A 1 255 VAL 255 255 VAL VAL A . A 1 256 TYR 256 256 TYR TYR A . A 1 257 GLU 257 257 GLU GLU A . A 1 258 ALA 258 258 ALA ALA A . A 1 259 ALA 259 259 ALA ALA A . A 1 260 ASN 260 260 ASN ASN A . A 1 261 LYS 261 261 LYS LYS A . A 1 262 VAL 262 262 VAL VAL A . A 1 263 PHE 263 263 PHE PHE A . A 1 264 ASN 264 264 ASN ASN A . A 1 265 GLY 265 265 GLY GLY A . A 1 266 GLY 266 266 GLY GLY A . A 1 267 ALA 267 267 ALA ALA A . A 1 268 VAL 268 268 VAL VAL A . A 1 269 LYS 269 269 LYS LYS A . A 1 270 GLY 270 270 GLY GLY A . A 1 271 TRP 271 271 TRP TRP A . # # loop_ # #