data_9A2Y # _entry.id 9A2Y # 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_00000183 PDBDEV_00000183 ? PDB 9A2Y pdb_00009a2y 10.2210/pdb9a2y/pdb # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 9A2Y _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 9A2Y # 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" "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 45869.055 _entity.id 1 _entity.pdbx_description P02931 _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 MMKRNILAVIVPALLVAGTANAAEIYNKDGNKVDLYGKAVGLHYFSKGNGENSYGGNGDMTYARLGFKGETQINSDLTGYGQWEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDYGRNYGVVYDALGYTDMLPEFGGDTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYLGKNERDTARRSNGDGVGGSISYEYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAANYGETRNATPITNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGATYYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVYQF _entity_poly.pdbx_seq_one_letter_code_can MMKRNILAVIVPALLVAGTANAAEIYNKDGNKVDLYGKAVGLHYFSKGNGENSYGGNGDMTYARLGFKGETQINSDLTGYGQWEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDYGRNYGVVYDALGYTDMLPEFGGDTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYLGKNERDTARRSNGDGVGGSISYEYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAANYGETRNATPITNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGATYYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVYQF _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 . MET 2 1 . LYS 3 1 . ARG 4 1 . ASN 5 1 . ILE 6 1 . LEU 7 1 . ALA 8 1 . VAL 9 1 . ILE 10 1 . VAL 11 1 . PRO 12 1 . ALA 13 1 . LEU 14 1 . LEU 15 1 . VAL 16 1 . ALA 17 1 . GLY 18 1 . THR 19 1 . ALA 20 1 . ASN 21 1 . ALA 22 1 . ALA 23 1 . GLU 24 1 . ILE 25 1 . TYR 26 1 . ASN 27 1 . LYS 28 1 . ASP 29 1 . GLY 30 1 . ASN 31 1 . LYS 32 1 . VAL 33 1 . ASP 34 1 . LEU 35 1 . TYR 36 1 . GLY 37 1 . LYS 38 1 . ALA 39 1 . VAL 40 1 . GLY 41 1 . LEU 42 1 . HIS 43 1 . TYR 44 1 . PHE 45 1 . SER 46 1 . LYS 47 1 . GLY 48 1 . ASN 49 1 . GLY 50 1 . GLU 51 1 . ASN 52 1 . SER 53 1 . TYR 54 1 . GLY 55 1 . GLY 56 1 . ASN 57 1 . GLY 58 1 . ASP 59 1 . MET 60 1 . THR 61 1 . TYR 62 1 . ALA 63 1 . ARG 64 1 . LEU 65 1 . GLY 66 1 . PHE 67 1 . LYS 68 1 . GLY 69 1 . GLU 70 1 . THR 71 1 . GLN 72 1 . ILE 73 1 . ASN 74 1 . SER 75 1 . ASP 76 1 . LEU 77 1 . THR 78 1 . GLY 79 1 . TYR 80 1 . GLY 81 1 . GLN 82 1 . TRP 83 1 . GLU 84 1 . TYR 85 1 . ASN 86 1 . PHE 87 1 . GLN 88 1 . GLY 89 1 . ASN 90 1 . ASN 91 1 . SER 92 1 . GLU 93 1 . GLY 94 1 . ALA 95 1 . ASP 96 1 . ALA 97 1 . GLN 98 1 . THR 99 1 . GLY 100 1 . ASN 101 1 . LYS 102 1 . THR 103 1 . ARG 104 1 . LEU 105 1 . ALA 106 1 . PHE 107 1 . ALA 108 1 . GLY 109 1 . LEU 110 1 . LYS 111 1 . TYR 112 1 . ALA 113 1 . ASP 114 1 . VAL 115 1 . GLY 116 1 . SER 117 1 . PHE 118 1 . ASP 119 1 . TYR 120 1 . GLY 121 1 . ARG 122 1 . ASN 123 1 . TYR 124 1 . GLY 125 1 . VAL 126 1 . VAL 127 1 . TYR 128 1 . ASP 129 1 . ALA 130 1 . LEU 131 1 . GLY 132 1 . TYR 133 1 . THR 134 1 . ASP 135 1 . MET 136 1 . LEU 137 1 . PRO 138 1 . GLU 139 1 . PHE 140 1 . GLY 141 1 . GLY 142 1 . ASP 143 1 . THR 144 1 . ALA 145 1 . TYR 146 1 . SER 147 1 . ASP 148 1 . ASP 149 1 . PHE 150 1 . PHE 151 1 . VAL 152 1 . GLY 153 1 . ARG 154 1 . VAL 155 1 . GLY 156 1 . GLY 157 1 . VAL 158 1 . ALA 159 1 . THR 160 1 . TYR 161 1 . ARG 162 1 . ASN 163 1 . SER 164 1 . ASN 165 1 . PHE 166 1 . PHE 167 1 . GLY 168 1 . LEU 169 1 . VAL 170 1 . ASP 171 1 . GLY 172 1 . LEU 173 1 . ASN 174 1 . PHE 175 1 . ALA 176 1 . VAL 177 1 . GLN 178 1 . TYR 179 1 . LEU 180 1 . GLY 181 1 . LYS 182 1 . ASN 183 1 . GLU 184 1 . ARG 185 1 . ASP 186 1 . THR 187 1 . ALA 188 1 . ARG 189 1 . ARG 190 1 . SER 191 1 . ASN 192 1 . GLY 193 1 . ASP 194 1 . GLY 195 1 . VAL 196 1 . GLY 197 1 . GLY 198 1 . SER 199 1 . ILE 200 1 . SER 201 1 . TYR 202 1 . GLU 203 1 . TYR 204 1 . GLU 205 1 . GLY 206 1 . PHE 207 1 . GLY 208 1 . ILE 209 1 . VAL 210 1 . GLY 211 1 . ALA 212 1 . TYR 213 1 . GLY 214 1 . ALA 215 1 . ALA 216 1 . ASP 217 1 . ARG 218 1 . THR 219 1 . ASN 220 1 . LEU 221 1 . GLN 222 1 . GLU 223 1 . ALA 224 1 . GLN 225 1 . PRO 226 1 . LEU 227 1 . GLY 228 1 . ASN 229 1 . GLY 230 1 . LYS 231 1 . LYS 232 1 . ALA 233 1 . GLU 234 1 . GLN 235 1 . TRP 236 1 . ALA 237 1 . THR 238 1 . GLY 239 1 . LEU 240 1 . LYS 241 1 . TYR 242 1 . ASP 243 1 . ALA 244 1 . ASN 245 1 . ASN 246 1 . ILE 247 1 . TYR 248 1 . LEU 249 1 . ALA 250 1 . ALA 251 1 . ASN 252 1 . TYR 253 1 . GLY 254 1 . GLU 255 1 . THR 256 1 . ARG 257 1 . ASN 258 1 . ALA 259 1 . THR 260 1 . PRO 261 1 . ILE 262 1 . THR 263 1 . ASN 264 1 . LYS 265 1 . PHE 266 1 . THR 267 1 . ASN 268 1 . THR 269 1 . SER 270 1 . GLY 271 1 . PHE 272 1 . ALA 273 1 . ASN 274 1 . LYS 275 1 . THR 276 1 . GLN 277 1 . ASP 278 1 . VAL 279 1 . LEU 280 1 . LEU 281 1 . VAL 282 1 . ALA 283 1 . GLN 284 1 . TYR 285 1 . GLN 286 1 . PHE 287 1 . ASP 288 1 . PHE 289 1 . GLY 290 1 . LEU 291 1 . ARG 292 1 . PRO 293 1 . SER 294 1 . ILE 295 1 . ALA 296 1 . TYR 297 1 . THR 298 1 . LYS 299 1 . SER 300 1 . LYS 301 1 . ALA 302 1 . LYS 303 1 . ASP 304 1 . VAL 305 1 . GLU 306 1 . GLY 307 1 . ILE 308 1 . GLY 309 1 . ASP 310 1 . VAL 311 1 . ASP 312 1 . LEU 313 1 . VAL 314 1 . ASN 315 1 . TYR 316 1 . PHE 317 1 . GLU 318 1 . VAL 319 1 . GLY 320 1 . ALA 321 1 . THR 322 1 . TYR 323 1 . TYR 324 1 . PHE 325 1 . ASN 326 1 . LYS 327 1 . ASN 328 1 . MET 329 1 . SER 330 1 . THR 331 1 . TYR 332 1 . VAL 333 1 . ASP 334 1 . TYR 335 1 . ILE 336 1 . ILE 337 1 . ASN 338 1 . GLN 339 1 . ILE 340 1 . ASP 341 1 . SER 342 1 . ASP 343 1 . ASN 344 1 . LYS 345 1 . LEU 346 1 . GLY 347 1 . VAL 348 1 . GLY 349 1 . SER 350 1 . ASP 351 1 . ASP 352 1 . THR 353 1 . VAL 354 1 . ALA 355 1 . VAL 356 1 . GLY 357 1 . ILE 358 1 . VAL 359 1 . TYR 360 1 . GLN 361 1 . PHE 362 # _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 GLY 1 . P02931 P02931 1 1 1 1 1 L-Photo-Leucine 227 309 LEU VAL 1 . P02931 P02931 1 1 2 2 1 L-Photo-Leucine 227 311 LEU GLU 1 . P02931 P02931 1 1 3 3 1 L-Photo-Leucine 227 306 LEU ASP 1 . P02931 P02931 1 1 4 4 1 L-Photo-Leucine 227 304 GLN LEU 1 . P02931 P02931 1 1 5 5 1 L-Photo-Leucine 225 313 LEU ILE 1 . P02931 P02931 1 1 6 6 1 L-Photo-Leucine 227 308 LEU PHE 1 . P02931 P02931 1 1 7 7 1 L-Photo-Leucine 42 140 LEU GLU 1 . P02931 P02931 1 1 8 8 1 L-Photo-Leucine 42 139 LEU ASP 1 . P02931 P02931 1 1 9 9 1 L-Photo-Leucine 227 312 LEU ASP 1 . P02931 P02931 1 1 10 10 1 L-Photo-Leucine 227 310 LEU LEU 1 . P02931 P02931 1 1 11 11 1 L-Photo-Leucine 227 313 LEU PRO 1 . P02931 P02931 1 1 12 12 1 L-Photo-Leucine 42 138 SER LEU 1 . P02931 P02931 1 1 13 13 1 L-Photo-Leucine 46 131 SER LEU 1 . P02931 P02931 1 1 14 14 1 L-Photo-Leucine 46 137 LEU TYR 1 . P02931 P02931 1 1 15 15 1 L-Photo-Leucine 227 316 LEU ASN 1 . P02931 P02931 1 1 16 16 1 L-Photo-Leucine 227 315 LEU GLU 1 . P02931 P02931 1 1 17 17 1 L-Photo-Leucine 221 318 LEU ASP 1 . P02931 P02931 1 1 18 18 1 L-Photo-Leucine 42 143 # 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 GLY . 10 1 1 1 1 by-residue NO 0.05 "upper bound" 227 309 . . A A . . LEU VAL . 10 1 1 2 2 by-residue NO 0.05 "upper bound" 227 311 . . A A . . LEU GLU . 10 1 1 3 3 by-residue NO 0.05 "upper bound" 227 306 . . A A . . LEU ASP . 10 1 1 4 4 by-residue NO 0.05 "upper bound" 227 304 . . A A . . GLN LEU . 10 1 1 5 5 by-residue NO 0.05 "upper bound" 225 313 . . A A . . LEU ILE . 10 1 1 6 6 by-residue NO 0.05 "upper bound" 227 308 . . A A . . LEU PHE . 10 1 1 7 7 by-residue NO 0.05 "upper bound" 42 140 . . A A . . LEU GLU . 10 1 1 8 8 by-residue NO 0.05 "upper bound" 42 139 . . A A . . LEU ASP . 10 1 1 9 9 by-residue NO 0.05 "upper bound" 227 312 . . A A . . LEU ASP . 10 1 1 10 10 by-residue NO 0.05 "upper bound" 227 310 . . A A . . LEU LEU . 10 1 1 11 11 by-residue NO 0.05 "upper bound" 227 313 . . A A . . LEU PRO . 10 1 1 12 12 by-residue NO 0.05 "upper bound" 42 138 . . A A . . SER LEU . 10 1 1 13 13 by-residue NO 0.05 "upper bound" 46 131 . . A A . . SER LEU . 10 1 1 14 14 by-residue NO 0.05 "upper bound" 46 137 . . A A . . LEU TYR . 10 1 1 15 15 by-residue NO 0.05 "upper bound" 227 316 . . A A . . LEU ASN . 10 1 1 16 16 by-residue NO 0.05 "upper bound" 227 315 . . A A . . LEU GLU . 10 1 1 17 17 by-residue NO 0.05 "upper bound" 221 318 . . A A . . LEU ASP . 10 1 1 18 18 by-residue NO 0.05 "upper bound" 42 143 . . # _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 PHE _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 362 # _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 P02931 _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 P02931 _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 9A2Y _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 OmpF by in-cell photo-crosslinking MS and deep learning" _struct.pdbx_structure_determination_methodology integrative # _struct_asym.details P02931 _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 OMPF_ECOLI _struct_ref.db_name UNP _struct_ref.details "Outer membrane porin F OS=Escherichia coli (strain K12) OX=83333 GN=ompF PE=1 SV=1" _struct_ref.entity_id 1 _struct_ref.id 1 _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_accession P02931 _struct_ref.pdbx_seq_one_letter_code MMKRNILAVIVPALLVAGTANAAEIYNKDGNKVDLYGKAVGLHYFSKGNGENSYGGNGDMTYARLGFKGETQINSDLTGYGQWEYNFQGNNSEGADAQTGNKTRLAFAGLKYADVGSFDYGRNYGVVYDALGYTDMLPEFGGDTAYSDDFFVGRVGGVATYRNSNFFGLVDGLNFAVQYLGKNERDTARRSNGDGVGGSISYEYEGFGIVGAYGAADRTNLQEAQPLGNGKKAEQWATGLKYDANNIYLAANYGETRNATPITNKFTNTSGFANKTQDVLLVAQYQFDFGLRPSIAYTKSKAKDVEGIGDVDLVNYFEVGATYYFNKNMSTYVDYIINQIDSDNKLGVGSDDTVAVGIVYQF # _struct_ref_seq.align_id 1 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.db_align_end 362 _struct_ref_seq.ref_id 1 _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.seq_align_end 362 # 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 MET 2 2 MET MET A . A 1 3 LYS 3 3 LYS LYS A . A 1 4 ARG 4 4 ARG ARG A . A 1 5 ASN 5 5 ASN ASN A . A 1 6 ILE 6 6 ILE ILE A . A 1 7 LEU 7 7 LEU LEU A . A 1 8 ALA 8 8 ALA ALA A . A 1 9 VAL 9 9 VAL VAL A . A 1 10 ILE 10 10 ILE ILE A . A 1 11 VAL 11 11 VAL VAL A . A 1 12 PRO 12 12 PRO PRO A . A 1 13 ALA 13 13 ALA ALA A . A 1 14 LEU 14 14 LEU LEU A . A 1 15 LEU 15 15 LEU LEU A . A 1 16 VAL 16 16 VAL VAL A . A 1 17 ALA 17 17 ALA ALA A . A 1 18 GLY 18 18 GLY GLY A . A 1 19 THR 19 19 THR THR A . A 1 20 ALA 20 20 ALA ALA A . A 1 21 ASN 21 21 ASN ASN A . A 1 22 ALA 22 22 ALA ALA A . A 1 23 ALA 23 23 ALA ALA A . A 1 24 GLU 24 24 GLU GLU A . A 1 25 ILE 25 25 ILE ILE A . A 1 26 TYR 26 26 TYR TYR A . A 1 27 ASN 27 27 ASN ASN A . A 1 28 LYS 28 28 LYS LYS A . A 1 29 ASP 29 29 ASP ASP A . A 1 30 GLY 30 30 GLY GLY A . A 1 31 ASN 31 31 ASN ASN A . A 1 32 LYS 32 32 LYS LYS A . A 1 33 VAL 33 33 VAL VAL A . A 1 34 ASP 34 34 ASP ASP A . A 1 35 LEU 35 35 LEU LEU A . A 1 36 TYR 36 36 TYR TYR A . A 1 37 GLY 37 37 GLY GLY A . A 1 38 LYS 38 38 LYS LYS A . A 1 39 ALA 39 39 ALA ALA A . A 1 40 VAL 40 40 VAL VAL A . A 1 41 GLY 41 41 GLY GLY A . A 1 42 LEU 42 42 LEU LEU A . A 1 43 HIS 43 43 HIS HIS A . A 1 44 TYR 44 44 TYR TYR A . A 1 45 PHE 45 45 PHE PHE A . A 1 46 SER 46 46 SER SER A . A 1 47 LYS 47 47 LYS LYS A . A 1 48 GLY 48 48 GLY GLY A . A 1 49 ASN 49 49 ASN ASN A . A 1 50 GLY 50 50 GLY GLY A . A 1 51 GLU 51 51 GLU GLU A . A 1 52 ASN 52 52 ASN ASN A . A 1 53 SER 53 53 SER SER A . A 1 54 TYR 54 54 TYR TYR A . A 1 55 GLY 55 55 GLY GLY A . A 1 56 GLY 56 56 GLY GLY A . A 1 57 ASN 57 57 ASN ASN A . A 1 58 GLY 58 58 GLY GLY A . A 1 59 ASP 59 59 ASP ASP A . A 1 60 MET 60 60 MET MET A . A 1 61 THR 61 61 THR THR A . A 1 62 TYR 62 62 TYR TYR A . A 1 63 ALA 63 63 ALA ALA A . A 1 64 ARG 64 64 ARG ARG A . A 1 65 LEU 65 65 LEU LEU A . A 1 66 GLY 66 66 GLY GLY A . A 1 67 PHE 67 67 PHE PHE A . A 1 68 LYS 68 68 LYS LYS A . A 1 69 GLY 69 69 GLY GLY A . A 1 70 GLU 70 70 GLU GLU A . A 1 71 THR 71 71 THR THR A . A 1 72 GLN 72 72 GLN GLN A . A 1 73 ILE 73 73 ILE ILE A . A 1 74 ASN 74 74 ASN ASN A . A 1 75 SER 75 75 SER SER A . A 1 76 ASP 76 76 ASP ASP A . A 1 77 LEU 77 77 LEU LEU A . A 1 78 THR 78 78 THR THR A . A 1 79 GLY 79 79 GLY GLY A . A 1 80 TYR 80 80 TYR TYR A . A 1 81 GLY 81 81 GLY GLY A . A 1 82 GLN 82 82 GLN GLN A . A 1 83 TRP 83 83 TRP TRP A . A 1 84 GLU 84 84 GLU GLU A . A 1 85 TYR 85 85 TYR TYR A . A 1 86 ASN 86 86 ASN ASN A . A 1 87 PHE 87 87 PHE PHE A . A 1 88 GLN 88 88 GLN GLN A . A 1 89 GLY 89 89 GLY GLY A . A 1 90 ASN 90 90 ASN ASN A . A 1 91 ASN 91 91 ASN ASN A . A 1 92 SER 92 92 SER SER A . A 1 93 GLU 93 93 GLU GLU A . A 1 94 GLY 94 94 GLY GLY A . A 1 95 ALA 95 95 ALA ALA A . A 1 96 ASP 96 96 ASP ASP A . A 1 97 ALA 97 97 ALA ALA A . A 1 98 GLN 98 98 GLN GLN A . A 1 99 THR 99 99 THR THR A . A 1 100 GLY 100 100 GLY GLY A . A 1 101 ASN 101 101 ASN ASN A . A 1 102 LYS 102 102 LYS LYS A . A 1 103 THR 103 103 THR THR A . A 1 104 ARG 104 104 ARG ARG A . A 1 105 LEU 105 105 LEU LEU A . A 1 106 ALA 106 106 ALA ALA A . A 1 107 PHE 107 107 PHE PHE A . A 1 108 ALA 108 108 ALA ALA A . A 1 109 GLY 109 109 GLY GLY A . A 1 110 LEU 110 110 LEU LEU A . A 1 111 LYS 111 111 LYS LYS A . A 1 112 TYR 112 112 TYR TYR A . A 1 113 ALA 113 113 ALA ALA A . A 1 114 ASP 114 114 ASP ASP A . A 1 115 VAL 115 115 VAL VAL A . A 1 116 GLY 116 116 GLY GLY A . A 1 117 SER 117 117 SER SER A . A 1 118 PHE 118 118 PHE PHE A . A 1 119 ASP 119 119 ASP ASP A . A 1 120 TYR 120 120 TYR TYR A . A 1 121 GLY 121 121 GLY GLY A . A 1 122 ARG 122 122 ARG ARG A . A 1 123 ASN 123 123 ASN ASN A . A 1 124 TYR 124 124 TYR TYR A . A 1 125 GLY 125 125 GLY GLY A . A 1 126 VAL 126 126 VAL VAL A . A 1 127 VAL 127 127 VAL VAL A . A 1 128 TYR 128 128 TYR TYR A . A 1 129 ASP 129 129 ASP ASP A . A 1 130 ALA 130 130 ALA ALA A . A 1 131 LEU 131 131 LEU LEU A . A 1 132 GLY 132 132 GLY GLY A . A 1 133 TYR 133 133 TYR TYR A . A 1 134 THR 134 134 THR THR A . A 1 135 ASP 135 135 ASP ASP A . A 1 136 MET 136 136 MET MET A . A 1 137 LEU 137 137 LEU LEU A . A 1 138 PRO 138 138 PRO PRO A . A 1 139 GLU 139 139 GLU GLU A . A 1 140 PHE 140 140 PHE PHE A . A 1 141 GLY 141 141 GLY GLY A . A 1 142 GLY 142 142 GLY GLY A . A 1 143 ASP 143 143 ASP ASP A . A 1 144 THR 144 144 THR THR A . A 1 145 ALA 145 145 ALA ALA A . A 1 146 TYR 146 146 TYR TYR A . A 1 147 SER 147 147 SER SER A . A 1 148 ASP 148 148 ASP ASP A . A 1 149 ASP 149 149 ASP ASP A . A 1 150 PHE 150 150 PHE PHE A . A 1 151 PHE 151 151 PHE PHE A . A 1 152 VAL 152 152 VAL VAL A . A 1 153 GLY 153 153 GLY GLY A . A 1 154 ARG 154 154 ARG ARG A . A 1 155 VAL 155 155 VAL VAL A . A 1 156 GLY 156 156 GLY GLY A . A 1 157 GLY 157 157 GLY GLY A . A 1 158 VAL 158 158 VAL VAL A . A 1 159 ALA 159 159 ALA ALA A . A 1 160 THR 160 160 THR THR A . A 1 161 TYR 161 161 TYR TYR A . A 1 162 ARG 162 162 ARG ARG A . A 1 163 ASN 163 163 ASN ASN A . A 1 164 SER 164 164 SER SER A . A 1 165 ASN 165 165 ASN ASN A . A 1 166 PHE 166 166 PHE PHE A . A 1 167 PHE 167 167 PHE PHE A . A 1 168 GLY 168 168 GLY GLY A . A 1 169 LEU 169 169 LEU LEU A . A 1 170 VAL 170 170 VAL VAL A . A 1 171 ASP 171 171 ASP ASP A . A 1 172 GLY 172 172 GLY GLY A . A 1 173 LEU 173 173 LEU LEU A . A 1 174 ASN 174 174 ASN ASN A . A 1 175 PHE 175 175 PHE PHE A . A 1 176 ALA 176 176 ALA ALA A . A 1 177 VAL 177 177 VAL VAL A . A 1 178 GLN 178 178 GLN GLN A . A 1 179 TYR 179 179 TYR TYR A . A 1 180 LEU 180 180 LEU LEU A . A 1 181 GLY 181 181 GLY GLY A . A 1 182 LYS 182 182 LYS LYS A . A 1 183 ASN 183 183 ASN ASN A . A 1 184 GLU 184 184 GLU GLU A . A 1 185 ARG 185 185 ARG ARG A . A 1 186 ASP 186 186 ASP ASP A . A 1 187 THR 187 187 THR THR A . A 1 188 ALA 188 188 ALA ALA A . A 1 189 ARG 189 189 ARG ARG A . A 1 190 ARG 190 190 ARG ARG A . A 1 191 SER 191 191 SER SER A . A 1 192 ASN 192 192 ASN ASN A . A 1 193 GLY 193 193 GLY GLY A . A 1 194 ASP 194 194 ASP ASP A . A 1 195 GLY 195 195 GLY GLY A . A 1 196 VAL 196 196 VAL VAL A . A 1 197 GLY 197 197 GLY GLY A . A 1 198 GLY 198 198 GLY GLY A . A 1 199 SER 199 199 SER SER A . A 1 200 ILE 200 200 ILE ILE A . A 1 201 SER 201 201 SER SER A . A 1 202 TYR 202 202 TYR TYR A . A 1 203 GLU 203 203 GLU GLU A . A 1 204 TYR 204 204 TYR TYR A . A 1 205 GLU 205 205 GLU GLU A . A 1 206 GLY 206 206 GLY GLY A . A 1 207 PHE 207 207 PHE PHE A . A 1 208 GLY 208 208 GLY GLY A . A 1 209 ILE 209 209 ILE ILE A . A 1 210 VAL 210 210 VAL VAL A . A 1 211 GLY 211 211 GLY GLY A . A 1 212 ALA 212 212 ALA ALA A . A 1 213 TYR 213 213 TYR TYR A . A 1 214 GLY 214 214 GLY GLY A . A 1 215 ALA 215 215 ALA ALA A . A 1 216 ALA 216 216 ALA ALA A . A 1 217 ASP 217 217 ASP ASP A . A 1 218 ARG 218 218 ARG ARG A . A 1 219 THR 219 219 THR THR A . A 1 220 ASN 220 220 ASN ASN A . A 1 221 LEU 221 221 LEU LEU A . A 1 222 GLN 222 222 GLN GLN A . A 1 223 GLU 223 223 GLU GLU A . A 1 224 ALA 224 224 ALA ALA A . A 1 225 GLN 225 225 GLN GLN A . A 1 226 PRO 226 226 PRO PRO A . A 1 227 LEU 227 227 LEU LEU A . A 1 228 GLY 228 228 GLY GLY A . A 1 229 ASN 229 229 ASN ASN A . A 1 230 GLY 230 230 GLY GLY A . A 1 231 LYS 231 231 LYS LYS A . A 1 232 LYS 232 232 LYS LYS A . A 1 233 ALA 233 233 ALA ALA A . A 1 234 GLU 234 234 GLU GLU A . A 1 235 GLN 235 235 GLN GLN A . A 1 236 TRP 236 236 TRP TRP A . A 1 237 ALA 237 237 ALA ALA A . A 1 238 THR 238 238 THR THR A . A 1 239 GLY 239 239 GLY GLY A . A 1 240 LEU 240 240 LEU LEU A . A 1 241 LYS 241 241 LYS LYS A . A 1 242 TYR 242 242 TYR TYR A . A 1 243 ASP 243 243 ASP ASP A . A 1 244 ALA 244 244 ALA ALA A . A 1 245 ASN 245 245 ASN ASN A . A 1 246 ASN 246 246 ASN ASN A . A 1 247 ILE 247 247 ILE ILE A . A 1 248 TYR 248 248 TYR TYR A . A 1 249 LEU 249 249 LEU LEU A . A 1 250 ALA 250 250 ALA ALA A . A 1 251 ALA 251 251 ALA ALA A . A 1 252 ASN 252 252 ASN ASN A . A 1 253 TYR 253 253 TYR TYR A . A 1 254 GLY 254 254 GLY GLY A . A 1 255 GLU 255 255 GLU GLU A . A 1 256 THR 256 256 THR THR A . A 1 257 ARG 257 257 ARG ARG A . A 1 258 ASN 258 258 ASN ASN A . A 1 259 ALA 259 259 ALA ALA A . A 1 260 THR 260 260 THR THR A . A 1 261 PRO 261 261 PRO PRO A . A 1 262 ILE 262 262 ILE ILE A . A 1 263 THR 263 263 THR THR A . A 1 264 ASN 264 264 ASN ASN A . A 1 265 LYS 265 265 LYS LYS A . A 1 266 PHE 266 266 PHE PHE A . A 1 267 THR 267 267 THR THR A . A 1 268 ASN 268 268 ASN ASN A . A 1 269 THR 269 269 THR THR A . A 1 270 SER 270 270 SER SER A . A 1 271 GLY 271 271 GLY GLY A . A 1 272 PHE 272 272 PHE PHE A . A 1 273 ALA 273 273 ALA ALA A . A 1 274 ASN 274 274 ASN ASN A . A 1 275 LYS 275 275 LYS LYS A . A 1 276 THR 276 276 THR THR A . A 1 277 GLN 277 277 GLN GLN A . A 1 278 ASP 278 278 ASP ASP A . A 1 279 VAL 279 279 VAL VAL A . A 1 280 LEU 280 280 LEU LEU A . A 1 281 LEU 281 281 LEU LEU A . A 1 282 VAL 282 282 VAL VAL A . A 1 283 ALA 283 283 ALA ALA A . A 1 284 GLN 284 284 GLN GLN A . A 1 285 TYR 285 285 TYR TYR A . A 1 286 GLN 286 286 GLN GLN A . A 1 287 PHE 287 287 PHE PHE A . A 1 288 ASP 288 288 ASP ASP A . A 1 289 PHE 289 289 PHE PHE A . A 1 290 GLY 290 290 GLY GLY A . A 1 291 LEU 291 291 LEU LEU A . A 1 292 ARG 292 292 ARG ARG A . A 1 293 PRO 293 293 PRO PRO A . A 1 294 SER 294 294 SER SER A . A 1 295 ILE 295 295 ILE ILE A . A 1 296 ALA 296 296 ALA ALA A . A 1 297 TYR 297 297 TYR TYR A . A 1 298 THR 298 298 THR THR A . A 1 299 LYS 299 299 LYS LYS A . A 1 300 SER 300 300 SER SER A . A 1 301 LYS 301 301 LYS LYS A . A 1 302 ALA 302 302 ALA ALA A . A 1 303 LYS 303 303 LYS LYS A . A 1 304 ASP 304 304 ASP ASP A . A 1 305 VAL 305 305 VAL VAL A . A 1 306 GLU 306 306 GLU GLU A . A 1 307 GLY 307 307 GLY GLY A . A 1 308 ILE 308 308 ILE ILE A . A 1 309 GLY 309 309 GLY GLY A . A 1 310 ASP 310 310 ASP ASP A . A 1 311 VAL 311 311 VAL VAL A . A 1 312 ASP 312 312 ASP ASP A . A 1 313 LEU 313 313 LEU LEU A . A 1 314 VAL 314 314 VAL VAL A . A 1 315 ASN 315 315 ASN ASN A . A 1 316 TYR 316 316 TYR TYR A . A 1 317 PHE 317 317 PHE PHE A . A 1 318 GLU 318 318 GLU GLU A . A 1 319 VAL 319 319 VAL VAL A . A 1 320 GLY 320 320 GLY GLY A . A 1 321 ALA 321 321 ALA ALA A . A 1 322 THR 322 322 THR THR A . A 1 323 TYR 323 323 TYR TYR A . A 1 324 TYR 324 324 TYR TYR A . A 1 325 PHE 325 325 PHE PHE A . A 1 326 ASN 326 326 ASN ASN A . A 1 327 LYS 327 327 LYS LYS A . A 1 328 ASN 328 328 ASN ASN A . A 1 329 MET 329 329 MET MET A . A 1 330 SER 330 330 SER SER A . A 1 331 THR 331 331 THR THR A . A 1 332 TYR 332 332 TYR TYR A . A 1 333 VAL 333 333 VAL VAL A . A 1 334 ASP 334 334 ASP ASP A . A 1 335 TYR 335 335 TYR TYR A . A 1 336 ILE 336 336 ILE ILE A . A 1 337 ILE 337 337 ILE ILE A . A 1 338 ASN 338 338 ASN ASN A . A 1 339 GLN 339 339 GLN GLN A . A 1 340 ILE 340 340 ILE ILE A . A 1 341 ASP 341 341 ASP ASP A . A 1 342 SER 342 342 SER SER A . A 1 343 ASP 343 343 ASP ASP A . A 1 344 ASN 344 344 ASN ASN A . A 1 345 LYS 345 345 LYS LYS A . A 1 346 LEU 346 346 LEU LEU A . A 1 347 GLY 347 347 GLY GLY A . A 1 348 VAL 348 348 VAL VAL A . A 1 349 GLY 349 349 GLY GLY A . A 1 350 SER 350 350 SER SER A . A 1 351 ASP 351 351 ASP ASP A . A 1 352 ASP 352 352 ASP ASP A . A 1 353 THR 353 353 THR THR A . A 1 354 VAL 354 354 VAL VAL A . A 1 355 ALA 355 355 ALA ALA A . A 1 356 VAL 356 356 VAL VAL A . A 1 357 GLY 357 357 GLY GLY A . A 1 358 ILE 358 358 ILE ILE A . A 1 359 VAL 359 359 VAL VAL A . A 1 360 TYR 360 360 TYR TYR A . A 1 361 GLN 361 361 GLN GLN A . A 1 362 PHE 362 362 PHE PHE A . # # loop_ # #