data_5M7J # _model_server_result.job_id vn6bmJIAgUTlwTm_8ptTxA _model_server_result.datetime_utc '2024-11-08 13:41:27' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 5m7j # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":402}' # _entry.id 5M7J # _exptl.entry_id 5M7J _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 887.199 _entity.id 8 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'BACTERIOPHEOPHYTIN B' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 5M7J _cell.length_a 57.9 _cell.length_b 84.8 _cell.length_c 384.3 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5M7J _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 8 M N N ? 8 R N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 D C FME 1 D FME 1 1_555 D N TYR 2 D TYR 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 A NE2 HIS 111 A HIS 91 1_555 E FE HEC . A HEC 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? metalc ? metalc2 A NE2 HIS 144 A HIS 124 1_555 H FE HEC . A HEC 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? metalc ? metalc3 A NE2 HIS 156 A HIS 136 1_555 F FE HEC . A HEC 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? metalc ? metalc4 A NE2 HIS 268 A HIS 248 1_555 G FE HEC . A HEC 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? metalc ? metalc5 A NE2 HIS 329 A HIS 309 1_555 H FE HEC . A HEC 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc6 B NE2 HIS 191 B HIS 190 1_555 P FE FE2 . B FE2 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? metalc ? metalc7 B NE2 HIS 231 B HIS 230 1_555 P FE FE2 . B FE2 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.622 ? metalc ? metalc8 P FE FE2 . B FE2 307 1_555 C NE2 HIS 218 C HIS 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? metalc ? metalc9 P FE FE2 . B FE2 307 1_555 C OE1 GLU 233 C GLU 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.602 ? metalc ? metalc10 P FE FE2 . B FE2 307 1_555 C OE2 GLU 233 C GLU 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? metalc ? metalc11 P FE FE2 . B FE2 307 1_555 C NE2 HIS 265 C HIS 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? # _chem_comp.formula 'C55 H74 N4 O6' _chem_comp.formula_weight 887.199 _chem_comp.id BPB _chem_comp.mon_nstd_flag . _chem_comp.name 'BACTERIOPHEOPHYTIN B' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C2 C1 BPB sing 218 n n C3 C2 BPB doub 219 e n C3 C4 BPB sing 220 n n C5 C3 BPB sing 221 n n C6 C5 BPB sing 222 n n C7 C6 BPB sing 223 n n C8 C7 BPB sing 224 n n C9 C8 BPB sing 225 n n NB C4B BPB sing 226 n y NC C1C BPB sing 227 n y NC C4C BPB doub 228 n y ND C1D BPB sing 229 n y C10 C8 BPB sing 230 n n C11 C10 BPB sing 231 n n C11 C12 BPB sing 232 n n C13 C12 BPB sing 233 n n C13 C14 BPB sing 234 n n C15 C13 BPB sing 235 n n C16 C15 BPB sing 236 n n C17 C16 BPB sing 237 n n C18 C17 BPB sing 238 n n C19 C18 BPB sing 239 n n C1A NA BPB doub 240 n y C1A CHA BPB sing 241 n y C1B NB BPB sing 242 n y C1B C2B BPB doub 243 n y C1C C2C BPB sing 244 n n C1D CHD BPB doub 245 n y O1D CGD BPB doub 246 n n C20 C18 BPB sing 247 n n C2A C1A BPB sing 248 n n C2A CAA BPB sing 249 n n O2A C1 BPB sing 250 n n O2A CGA BPB sing 251 n n C2B C3B BPB sing 252 n y C2C CMC BPB sing 253 n n C2D C1D BPB sing 254 n y C2D CMD BPB sing 255 n n O2D CGD BPB sing 256 n n C3A C2A BPB sing 257 n n C3A C4A BPB sing 258 n n C3B C4B BPB doub 259 n y C3B CAB BPB sing 260 n n C3C C2C BPB sing 261 n n C3C CAC BPB doub 262 e n C3D C2D BPB doub 263 n y C4A NA BPB sing 264 n y C4A CHB BPB doub 265 n y C4B CHC BPB sing 266 n y C4C C3C BPB sing 267 n n C4D ND BPB sing 268 n y C4D C3D BPB sing 269 n y CAB CBB BPB sing 270 n n CAB OBB BPB doub 271 n n CAC CBC BPB sing 272 n n CAD C3D BPB sing 273 n n CBA CAA BPB sing 274 n n CBA CGA BPB sing 275 n n CBD CAD BPB sing 276 n n CBD CHA BPB sing 277 n n OBD CAD BPB doub 278 n n CED O2D BPB sing 279 n n CGA O1A BPB doub 280 n n CGD CBD BPB sing 281 n n CHA C4D BPB doub 282 n y CHB C1B BPB sing 283 n y CHC C1C BPB doub 284 n y CHD C4C BPB sing 285 n y CMA C3A BPB sing 286 n n CMB C2B BPB sing 287 n n C1 H1 BPB sing 288 n n C1 H1A BPB sing 289 n n C2 H2 BPB sing 290 n n C4 H4 BPB sing 291 n n C4 H4A BPB sing 292 n n C4 H4B BPB sing 293 n n C5 H5 BPB sing 294 n n C5 H5A BPB sing 295 n n C6 H6 BPB sing 296 n n C6 H6A BPB sing 297 n n C7 H7 BPB sing 298 n n C7 H7A BPB sing 299 n n C8 H8 BPB sing 300 n n C9 H9 BPB sing 301 n n C9 H9A BPB sing 302 n n C9 H9B BPB sing 303 n n NB H171 BPB sing 304 n n ND H181 BPB sing 305 n n C10 H10 BPB sing 306 n n C10 H10A BPB sing 307 n n C11 H11 BPB sing 308 n n C11 H11A BPB sing 309 n n C12 H12 BPB sing 310 n n C12 H12A BPB sing 311 n n C13 H13 BPB sing 312 n n C14 H14 BPB sing 313 n n C14 H14A BPB sing 314 n n C14 H14B BPB sing 315 n n C15 H15 BPB sing 316 n n C15 H15A BPB sing 317 n n C16 H16 BPB sing 318 n n C16 H16A BPB sing 319 n n C17 H17 BPB sing 320 n n C17 H17A BPB sing 321 n n C18 H18 BPB sing 322 n n C19 H19 BPB sing 323 n n C19 H19A BPB sing 324 n n C19 H19B BPB sing 325 n n C20 H20 BPB sing 326 n n C20 H20A BPB sing 327 n n C20 H20B BPB sing 328 n n C2A H42 BPB sing 329 n n C2C H43 BPB sing 330 n n C3A H44 BPB sing 331 n n CAA HAA BPB sing 332 n n CAA HAAA BPB sing 333 n n CAC HAC BPB sing 334 n n CBA HBA BPB sing 335 n n CBA HBAA BPB sing 336 n n CBB HBB BPB sing 337 n n CBB HBBA BPB sing 338 n n CBB HBBB BPB sing 339 n n CBC HBC BPB sing 340 n n CBC HBCA BPB sing 341 n n CBC H55 BPB sing 342 n n CBD HBD BPB sing 343 n n CED HED BPB sing 344 n n CED HEDA BPB sing 345 n n CED HEDB BPB sing 346 n n CHB HHB BPB sing 347 n n CHC HHC BPB sing 348 n n CHD HHD BPB sing 349 n n CMA HMA BPB sing 350 n n CMA HMAA BPB sing 351 n n CMA HMAB BPB sing 352 n n CMB HMB BPB sing 353 n n CMB HMBA BPB sing 354 n n CMB HMBB BPB sing 355 n n CMC HMC BPB sing 356 n n CMC HMCA BPB sing 357 n n CMC HMCB BPB sing 358 n n CMD HMD BPB sing 359 n n CMD HMDA BPB sing 360 n n CMD HMDB BPB sing 361 n n # _atom_sites.entry_id 5M7J _atom_sites.fract_transf_matrix[1][1] 0.017271 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011792 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.002602 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code E 5 HEC A 1 401 1333 HEC HEM . F 5 HEC A 1 402 1334 HEC HEM . G 5 HEC A 1 403 1335 HEC HEM . H 5 HEC A 1 404 1336 HEC HEM . I 6 DGA A 1 405 1278 DGA DGA . J 7 BCL B 1 301 1274 BCL BCL . K 7 BCL B 1 302 1275 BCL BCL . L 7 BCL B 1 303 1276 BCL BCL . M 8 BPB B 1 304 1277 BPB BPB . N 9 MPG B 1 305 1279 MPG MPG . O 9 MPG B 1 306 1280 MPG MPG . P 10 FE2 B 1 307 1326 FE2 FE2 . Q 7 BCL C 1 401 1324 BCL BCL . R 8 BPB C 1 402 1325 BPB BPB . S 11 MQ7 C 1 403 1327 MQ7 MQ7 . T 12 NS5 C 1 404 1328 NS5 NS5 . U 13 OTP C 1 405 1329 OTP OTP . V 9 MPG C 1 406 1330 MPG MPG . W 14 PO4 C 1 407 1331 PO4 PO4 . X 14 PO4 C 1 408 1332 PO4 PO4 . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C1 BPB . . . R 8 11.49 -38.08 42.996 1 57.08 ? C1 BPB 402 C 1 HETATM 2 C C2 BPB . . . R 8 10.669 -39.143 43.713 1 58.05 ? C2 BPB 402 C 1 HETATM 3 C C3 BPB . . . R 8 10.17 -40.203 43.122 1 59.01 ? C3 BPB 402 C 1 HETATM 4 C C4 BPB . . . R 8 10.329 -40.542 41.643 1 61.77 ? C4 BPB 402 C 1 HETATM 5 C C5 BPB . . . R 8 9.35 -41.219 43.921 1 59.11 ? C5 BPB 402 C 1 HETATM 6 C C6 BPB . . . R 8 8.296 -42.007 43.144 1 51.94 ? C6 BPB 402 C 1 HETATM 7 C C7 BPB . . . R 8 7.413 -42.829 44.081 1 49.71 ? C7 BPB 402 C 1 HETATM 8 C C8 BPB . . . R 8 6.534 -43.887 43.421 1 56.81 ? C8 BPB 402 C 1 HETATM 9 C C9 BPB . . . R 8 5.045 -43.68 43.77 1 71.35 ? C9 BPB 402 C 1 HETATM 10 N NA BPB . . . R 8 7.771 -31.156 41.887 1 61.42 ? NA BPB 402 C 1 HETATM 11 N NB BPB . . . R 8 7.031 -29.759 44.397 1 54.38 ? NB BPB 402 C 1 HETATM 12 N NC BPB . . . R 8 8.257 -27.197 43.423 1 53.61 ? NC BPB 402 C 1 HETATM 13 N ND BPB . . . R 8 8.933 -28.59 41.058 1 70.92 ? ND BPB 402 C 1 HETATM 14 C C10 BPB . . . R 8 7.015 -45.281 43.858 1 71.13 ? C10 BPB 402 C 1 HETATM 15 C C11 BPB . . . R 8 6.141 -46.324 44.557 1 72.13 ? C11 BPB 402 C 1 HETATM 16 C C12 BPB . . . R 8 6.127 -46.208 46.089 1 63.88 ? C12 BPB 402 C 1 HETATM 17 C C13 BPB . . . R 8 5.868 -47.542 46.816 1 67.12 ? C13 BPB 402 C 1 HETATM 18 C C14 BPB . . . R 8 4.397 -47.799 47.147 1 60.41 ? C14 BPB 402 C 1 HETATM 19 C C15 BPB . . . R 8 6.656 -47.445 48.129 1 72.16 ? C15 BPB 402 C 1 HETATM 20 C C16 BPB . . . R 8 6.674 -48.668 49.031 1 71.22 ? C16 BPB 402 C 1 HETATM 21 C C1A BPB . . . R 8 8.443 -31.681 40.794 1 61.71 ? C1A BPB 402 C 1 HETATM 22 O O1A BPB . . . R 8 11.827 -35.542 42.249 1 54.09 ? O1A BPB 402 C 1 HETATM 23 C C1B BPB . . . R 8 6.378 -30.97 44.619 1 56.31 ? C1B BPB 402 C 1 HETATM 24 C C1C BPB . . . R 8 7.762 -26.763 44.616 1 55.52 ? C1C BPB 402 C 1 HETATM 25 C C1D BPB . . . R 8 9.365 -27.338 40.598 1 69.61 ? C1D BPB 402 C 1 HETATM 26 O O1D BPB . . . R 8 8.959 -32.877 37.05 1 55.54 ? O1D BPB 402 C 1 HETATM 27 C C2A BPB . . . R 8 8.404 -33.179 40.803 1 59.27 ? C2A BPB 402 C 1 HETATM 28 O O2A BPB . . . R 8 10.496 -37.261 42.304 1 59.64 ? O2A BPB 402 C 1 HETATM 29 C C2B BPB . . . R 8 5.706 -30.947 45.847 1 58.8 ? C2B BPB 402 C 1 HETATM 30 C C2C BPB . . . R 8 7.912 -25.299 44.822 1 51.34 ? C2C BPB 402 C 1 HETATM 31 C C2D BPB . . . R 8 9.971 -27.443 39.319 1 62.99 ? C2D BPB 402 C 1 HETATM 32 O O2D BPB . . . R 8 7.769 -31.034 37.268 1 58.82 ? O2D BPB 402 C 1 HETATM 33 C C3A BPB . . . R 8 7.253 -33.469 41.78 1 56.5 ? C3A BPB 402 C 1 HETATM 34 C C3B BPB . . . R 8 5.931 -29.7 46.432 1 55.51 ? C3B BPB 402 C 1 HETATM 35 C C3C BPB . . . R 8 8.569 -24.835 43.503 1 47.05 ? C3C BPB 402 C 1 HETATM 36 C C3D BPB . . . R 8 9.903 -28.805 38.989 1 61.9 ? C3D BPB 402 C 1 HETATM 37 C C4A BPB . . . R 8 7.171 -32.205 42.57 1 56.73 ? C4A BPB 402 C 1 HETATM 38 C C4B BPB . . . R 8 6.763 -28.969 45.478 1 56.1 ? C4B BPB 402 C 1 HETATM 39 C C4C BPB . . . R 8 8.618 -26.097 42.681 1 54.69 ? C4C BPB 402 C 1 HETATM 40 C C4D BPB . . . R 8 9.278 -29.452 40.053 1 62.23 ? C4D BPB 402 C 1 HETATM 41 C CAA BPB . . . R 8 9.732 -33.809 41.25 1 54.13 ? CAA BPB 402 C 1 HETATM 42 C CAB BPB . . . R 8 5.443 -29.276 47.725 1 49.82 ? CAB BPB 402 C 1 HETATM 43 C CAC BPB . . . R 8 9.04 -23.563 43.109 1 45.94 ? CAC BPB 402 C 1 HETATM 44 C CAD BPB . . . R 8 10.238 -29.807 38.038 1 61.7 ? CAD BPB 402 C 1 HETATM 45 C CBA BPB . . . R 8 9.653 -35.34 41.295 1 55.95 ? CBA BPB 402 C 1 HETATM 46 C CBB BPB . . . R 8 5.034 -27.853 47.974 1 43.98 ? CBB BPB 402 C 1 HETATM 47 O OBB BPB . . . R 8 5.334 -30.058 48.686 1 49.07 ? OBB BPB 402 C 1 HETATM 48 C CBC BPB . . . R 8 8.947 -22.359 44.021 1 49 ? CBC BPB 402 C 1 HETATM 49 C CBD BPB . . . R 8 9.717 -31.176 38.56 1 58.95 ? CBD BPB 402 C 1 HETATM 50 O OBD BPB . . . R 8 10.838 -29.724 36.948 1 66.63 ? OBD BPB 402 C 1 HETATM 51 C CED BPB . . . R 8 6.812 -31.615 36.342 1 58.67 ? CED BPB 402 C 1 HETATM 52 C CGA BPB . . . R 8 10.786 -36.022 41.988 1 55.44 ? CGA BPB 402 C 1 HETATM 53 C CGD BPB . . . R 8 8.812 -31.788 37.572 1 57.47 ? CGD BPB 402 C 1 HETATM 54 C CHA BPB . . . R 8 9.107 -30.845 39.934 1 61.26 ? CHA BPB 402 C 1 HETATM 55 C CHB BPB . . . R 8 6.424 -32.037 43.716 1 54.68 ? CHB BPB 402 C 1 HETATM 56 C CHC BPB . . . R 8 7.287 -27.661 45.591 1 61.78 ? CHC BPB 402 C 1 HETATM 57 C CHD BPB . . . R 8 9.163 -26.175 41.413 1 65.29 ? CHD BPB 402 C 1 HETATM 58 C CMA BPB . . . R 8 5.942 -33.747 41.049 1 53.63 ? CMA BPB 402 C 1 HETATM 59 C CMB BPB . . . R 8 4.898 -32.118 46.375 1 59.52 ? CMB BPB 402 C 1 HETATM 60 C CMC BPB . . . R 8 6.582 -24.63 45.156 1 48.18 ? CMC BPB 402 C 1 HETATM 61 C CMD BPB . . . R 8 10.551 -26.295 38.523 1 56.88 ? CMD BPB 402 C 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 240 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 61 #