data_2O9B # _model_server_result.job_id cgCNjCpfsMv6oUxsFfKLCg _model_server_result.datetime_utc '2025-07-07 13:51:17' _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 2o9b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":328}' # _entry.id 2O9B # _exptl.entry_id 2O9B _exptl.method 'X-RAY DIFFRACTION' # _entity.details 'Biliverdin which was reduced to 2(R),3(E)-phytochromobilin upon ligation to the protien was obtained from Porphyrin Products (Logan, UT)' _entity.formula_weight 585.67 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 116.4 _cell.angle_gamma 90 _cell.entry_id 2O9B _cell.length_a 89.5 _cell.length_b 51.5 _cell.length_c 80.8 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2O9B _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 39 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 24 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id CBA _struct_conn.ptnr2_label_comp_id LBV _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id LBV _struct_conn.ptnr2_auth_seq_id 328 _struct_conn.ptnr2_symmetry 1_555 _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 1.76 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C33 H37 N4 O6 1' _chem_comp.formula_weight 585.67 _chem_comp.id LBV _chem_comp.mon_nstd_flag . _chem_comp.name '3-[2-[(Z)-[3-(2-carboxyethyl)-5-[(Z)-(4-ethenyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-4-methyl-pyrrol-1-ium -2-ylidene]methyl]-5-[(Z)-[(3E)-3-ethylidene-4-methyl-5-oxidanylidene-pyrrolidin-2-ylidene]methyl]-4-methyl-1H-pyrrol-3- yl]propanoic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '2(R),3(E)- PHYTOCHROMOBILIN' # 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 C1A N_A LBV sing 173 n n C1A C2A LBV sing 174 n n C1B C2B LBV doub 175 n y C1B CHB LBV sing 176 n n O1B CGB LBV doub 177 n n C1C CHC LBV doub 178 z n C1D CHD LBV doub 179 z n C2A CMA LBV sing 180 n n C2A C3A LBV sing 181 n n C2B CMB LBV sing 182 n n C2C C1C LBV sing 183 n n O2C CGC LBV doub 184 n n C2D C1D LBV sing 185 n n C2D CMD LBV sing 186 n n C3A CAA LBV doub 187 e n C3B C2B LBV sing 188 n y C3B CAB LBV sing 189 n n C3C C2C LBV doub 190 n n C3C C4C LBV sing 191 n n C3D C2D LBV doub 192 n n C4A C3A LBV sing 193 n n C4A CHB LBV doub 194 z n C4B C3B LBV doub 195 n y C4B N_B LBV sing 196 n y C4C N_C LBV doub 197 n n C4D C3D LBV sing 198 n n C4D N_D LBV sing 199 n n CAA CBA LBV sing 200 n n CAC C2C LBV sing 201 n n CAC CBC LBV sing 202 n n CAD C3D LBV sing 203 n n CBB CAB LBV sing 204 n n CBB CGB LBV sing 205 n n CBD CAD LBV doub 206 n n CGB O2B LBV sing 207 n n CGC O1C LBV sing 208 n n CGC CBC LBV sing 209 n n CHC C4B LBV sing 210 n n CHD C4C LBV sing 211 n n CMC C3C LBV sing 212 n n N_A C4A LBV sing 213 n n O_A C1A LBV doub 214 n n N_B C1B LBV sing 215 n y N_C C1C LBV sing 216 n n N_D C1D LBV sing 217 n n O_D C4D LBV doub 218 n n O1C HO1C LBV sing 219 n n C2A H2A LBV sing 220 n n O2B HO2B LBV sing 221 n n CAA HAA1 LBV sing 222 n n CAB HAB1 LBV sing 223 n n CAB HAB2 LBV sing 224 n n CAC HAC1 LBV sing 225 n n CAC HAC2 LBV sing 226 n n CAD HAD1 LBV sing 227 n n CBA HBA1 LBV sing 228 n n CBA HBA2 LBV sing 229 n n CBA HBA3 LBV sing 230 n n CBB HBB1 LBV sing 231 n n CBB HBB2 LBV sing 232 n n CBC HBC1 LBV sing 233 n n CBC HBC2 LBV sing 234 n n CBD HBD1 LBV sing 235 n n CBD HBD2 LBV sing 236 n n CHB HHB1 LBV sing 237 n n CHC HHC1 LBV sing 238 n n CHD HHD1 LBV sing 239 n n CMA HMA1 LBV sing 240 n n CMA HMA2 LBV sing 241 n n CMA HMA3 LBV sing 242 n n CMB HMB1 LBV sing 243 n n CMB HMB2 LBV sing 244 n n CMB HMB3 LBV sing 245 n n CMC HMC1 LBV sing 246 n n CMC HMC2 LBV sing 247 n n CMC HMC3 LBV sing 248 n n CMD HMD1 LBV sing 249 n n CMD HMD2 LBV sing 250 n n CMD HMD3 LBV sing 251 n n N_A HAD LBV sing 252 n n N_B HAE LBV sing 253 n n N_C HAF LBV sing 254 n n N_D HAG LBV sing 255 n n # _atom_sites.entry_id 2O9B _atom_sites.fract_transf_matrix[1][1] 0.011177 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005551 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019427 _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] 0.013809 _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 B 2 LBV A 1 328 328 LBV LBV . C 3 HOH A 1 329 1 HOH HOH . C 3 HOH A 2 330 2 HOH HOH . C 3 HOH A 3 331 3 HOH HOH . C 3 HOH A 4 332 4 HOH HOH . C 3 HOH A 5 333 5 HOH HOH . C 3 HOH A 6 334 6 HOH HOH . C 3 HOH A 7 335 7 HOH HOH . C 3 HOH A 8 336 8 HOH HOH . C 3 HOH A 9 337 9 HOH HOH . C 3 HOH A 10 338 10 HOH HOH . C 3 HOH A 11 339 11 HOH HOH . C 3 HOH A 12 340 12 HOH HOH . C 3 HOH A 13 341 13 HOH HOH . C 3 HOH A 14 342 14 HOH HOH . C 3 HOH A 15 343 15 HOH HOH . C 3 HOH A 16 344 16 HOH HOH . C 3 HOH A 17 345 17 HOH HOH . C 3 HOH A 18 346 18 HOH HOH . C 3 HOH A 19 347 19 HOH HOH . C 3 HOH A 20 348 20 HOH HOH . C 3 HOH A 21 349 21 HOH HOH . C 3 HOH A 22 350 22 HOH HOH . C 3 HOH A 23 351 23 HOH HOH . C 3 HOH A 24 352 24 HOH HOH . C 3 HOH A 25 353 25 HOH HOH . C 3 HOH A 26 354 26 HOH HOH . C 3 HOH A 27 355 27 HOH HOH . C 3 HOH A 28 356 28 HOH HOH . C 3 HOH A 29 357 29 HOH HOH . C 3 HOH A 30 358 30 HOH HOH . C 3 HOH A 31 359 31 HOH HOH . C 3 HOH A 32 360 32 HOH HOH . C 3 HOH A 33 361 33 HOH HOH . C 3 HOH A 34 362 34 HOH HOH . C 3 HOH A 35 363 35 HOH HOH . C 3 HOH A 36 364 36 HOH HOH . C 3 HOH A 37 365 37 HOH HOH . C 3 HOH A 38 366 38 HOH HOH . C 3 HOH A 39 367 39 HOH HOH . C 3 HOH A 40 368 40 HOH HOH . C 3 HOH A 41 369 41 HOH HOH . C 3 HOH A 42 370 42 HOH HOH . C 3 HOH A 43 371 43 HOH HOH . C 3 HOH A 44 372 44 HOH HOH . C 3 HOH A 45 373 45 HOH HOH . C 3 HOH A 46 374 46 HOH HOH . C 3 HOH A 47 375 47 HOH HOH . C 3 HOH A 48 376 48 HOH HOH . C 3 HOH A 49 377 49 HOH HOH . C 3 HOH A 50 378 50 HOH HOH . C 3 HOH A 51 379 51 HOH HOH . C 3 HOH A 52 380 52 HOH HOH . C 3 HOH A 53 381 53 HOH HOH . C 3 HOH A 54 382 54 HOH HOH . C 3 HOH A 55 383 55 HOH HOH . C 3 HOH A 56 384 56 HOH HOH . C 3 HOH A 57 385 57 HOH HOH . C 3 HOH A 58 386 58 HOH HOH . C 3 HOH A 59 387 59 HOH HOH . C 3 HOH A 60 388 60 HOH HOH . C 3 HOH A 61 389 61 HOH HOH . C 3 HOH A 62 390 62 HOH HOH . C 3 HOH A 63 391 63 HOH HOH . C 3 HOH A 64 392 64 HOH HOH . C 3 HOH A 65 393 65 HOH HOH . C 3 HOH A 66 394 66 HOH HOH . C 3 HOH A 67 395 67 HOH HOH . C 3 HOH A 68 396 68 HOH HOH . C 3 HOH A 69 397 69 HOH HOH . C 3 HOH A 70 398 70 HOH HOH . C 3 HOH A 71 399 71 HOH HOH . C 3 HOH A 72 400 72 HOH HOH . C 3 HOH A 73 401 73 HOH HOH . C 3 HOH A 74 402 74 HOH HOH . C 3 HOH A 75 403 75 HOH HOH . C 3 HOH A 76 404 76 HOH HOH . C 3 HOH A 77 405 77 HOH HOH . C 3 HOH A 78 406 78 HOH HOH . C 3 HOH A 79 407 79 HOH HOH . C 3 HOH A 80 408 80 HOH HOH . C 3 HOH A 81 409 81 HOH HOH . C 3 HOH A 82 410 82 HOH HOH . C 3 HOH A 83 411 83 HOH HOH . C 3 HOH A 84 412 84 HOH HOH . C 3 HOH A 85 413 85 HOH HOH . C 3 HOH A 86 414 86 HOH HOH . C 3 HOH A 87 415 87 HOH HOH . C 3 HOH A 88 416 88 HOH HOH . C 3 HOH A 89 417 89 HOH HOH . C 3 HOH A 90 418 90 HOH HOH . C 3 HOH A 91 419 91 HOH HOH . C 3 HOH A 92 420 92 HOH HOH . C 3 HOH A 93 421 93 HOH HOH . C 3 HOH A 94 422 94 HOH HOH . C 3 HOH A 95 423 95 HOH HOH . C 3 HOH A 96 424 96 HOH HOH . C 3 HOH A 97 425 97 HOH HOH . C 3 HOH A 98 426 98 HOH HOH . C 3 HOH A 99 427 99 HOH HOH . C 3 HOH A 100 428 100 HOH HOH . C 3 HOH A 101 429 101 HOH HOH . C 3 HOH A 102 430 102 HOH HOH . C 3 HOH A 103 431 103 HOH HOH . C 3 HOH A 104 432 104 HOH HOH . C 3 HOH A 105 433 105 HOH HOH . C 3 HOH A 106 434 106 HOH HOH . C 3 HOH A 107 435 107 HOH HOH . C 3 HOH A 108 436 108 HOH HOH . C 3 HOH A 109 437 109 HOH HOH . C 3 HOH A 110 438 110 HOH HOH . C 3 HOH A 111 439 111 HOH HOH . # 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 C1A LBV . . . B 2 23.768 -9.467 20.708 1 28.31 ? C1A LBV 328 A 1 HETATM 2 C C1B LBV . . . B 2 19.755 -7.483 20.9 1 20.91 ? C1B LBV 328 A 1 HETATM 3 O O1B LBV . . . B 2 15.418 -2.574 21.151 1 18.39 ? O1B LBV 328 A 1 HETATM 4 C C1C LBV . . . B 2 18.611 -7.052 16.567 1 20.33 ? C1C LBV 328 A 1 HETATM 5 O O1C LBV . . . B 2 17.002 -4.315 12.816 1 21.44 ? O1C LBV 328 A 1 HETATM 6 C C1D LBV . . . B 2 21.548 -8.6 13.185 1 24.01 ? C1D LBV 328 A 1 HETATM 7 C C2A LBV . . . B 2 24.13 -9.693 22.042 1 27.86 ? C2A LBV 328 A 1 HETATM 8 C C2B LBV . . . B 2 18.585 -6.813 21.402 1 21 ? C2B LBV 328 A 1 HETATM 9 O O2B LBV . . . B 2 14.544 -3.661 19.414 1 17.98 ? O2B LBV 328 A 1 HETATM 10 C C2C LBV . . . B 2 18.028 -6.793 15.317 1 20.5 ? C2C LBV 328 A 1 HETATM 11 O O2C LBV . . . B 2 18.19 -3.03 14.168 1 23 ? O2C LBV 328 A 1 HETATM 12 C C2D LBV . . . B 2 22.44 -9.647 12.618 1 25.8 ? C2D LBV 328 A 1 HETATM 13 C C3A LBV . . . B 2 22.879 -9.122 22.584 1 27.57 ? C3A LBV 328 A 1 HETATM 14 C C3B LBV . . . B 2 17.855 -6.46 20.309 1 18.99 ? C3B LBV 328 A 1 HETATM 15 C C3C LBV . . . B 2 18.895 -7.311 14.375 1 19.99 ? C3C LBV 328 A 1 HETATM 16 C C3D LBV . . . B 2 23.071 -9.015 11.523 1 24.94 ? C3D LBV 328 A 1 HETATM 17 C C4A LBV . . . B 2 21.846 -8.876 21.561 1 25.23 ? C4A LBV 328 A 1 HETATM 18 C C4B LBV . . . B 2 18.583 -6.918 19.174 1 20.64 ? C4B LBV 328 A 1 HETATM 19 C C4C LBV . . . B 2 19.966 -7.86 15.082 1 20.59 ? C4C LBV 328 A 1 HETATM 20 C C4D LBV . . . B 2 22.579 -7.685 11.505 1 24.67 ? C4D LBV 328 A 1 HETATM 21 C CAA LBV . . . B 2 22.466 -9.687 23.813 1 28.89 ? CAA LBV 328 A 1 HETATM 22 C CAB LBV . . . B 2 16.525 -5.736 20.301 1 20.91 ? CAB LBV 328 A 1 HETATM 23 C CAC LBV . . . B 2 16.697 -6.132 14.992 1 20.42 ? CAC LBV 328 A 1 HETATM 24 C CAD LBV . . . B 2 24.067 -9.605 10.582 1 28 ? CAD LBV 328 A 1 HETATM 25 C CBA LBV . . . B 2 23.368 -10.026 24.976 1 31.68 ? CBA LBV 328 A 1 HETATM 26 C CBB LBV . . . B 2 16.772 -4.229 20.044 1 16.04 ? CBB LBV 328 A 1 HETATM 27 C CBC LBV . . . B 2 16.718 -4.619 15.164 1 19.65 ? CBC LBV 328 A 1 HETATM 28 C CBD LBV . . . B 2 24.631 -8.896 9.581 1 25.95 ? CBD LBV 328 A 1 HETATM 29 C CGB LBV . . . B 2 15.494 -3.43 20.206 1 19.56 ? CGB LBV 328 A 1 HETATM 30 C CGC LBV . . . B 2 17.358 -3.953 13.962 1 22.64 ? CGC LBV 328 A 1 HETATM 31 C CHB LBV . . . B 2 20.849 -7.959 21.785 1 20.99 ? CHB LBV 328 A 1 HETATM 32 C CHC LBV . . . B 2 18.082 -6.724 17.849 1 19.97 ? CHC LBV 328 A 1 HETATM 33 C CHD LBV . . . B 2 21.153 -8.521 14.626 1 20.95 ? CHD LBV 328 A 1 HETATM 34 C CMA LBV . . . B 2 25.352 -8.849 22.417 1 28.24 ? CMA LBV 328 A 1 HETATM 35 C CMB LBV . . . B 2 18.219 -6.517 22.848 1 19.51 ? CMB LBV 328 A 1 HETATM 36 C CMC LBV . . . B 2 18.64 -7.269 12.902 1 20.11 ? CMC LBV 328 A 1 HETATM 37 C CMD LBV . . . B 2 22.567 -11.076 13.099 1 24.08 ? CMD LBV 328 A 1 HETATM 38 N N_A LBV . . . B 2 22.635 -8.742 20.394 1 26.33 ? N_A LBV 328 A 1 HETATM 39 O O_A LBV . . . B 2 24.717 -9.395 19.92 1 25.53 ? O_A LBV 328 A 1 HETATM 40 N N_B LBV . . . B 2 19.765 -7.542 19.519 1 20.52 ? N_B LBV 328 A 1 HETATM 41 N N_C LBV . . . B 2 19.811 -7.708 16.439 1 21.05 ? N_C LBV 328 A 1 HETATM 42 N N_D LBV . . . B 2 21.693 -7.384 12.492 1 23.39 ? N_D LBV 328 A 1 HETATM 43 O O_D LBV . . . B 2 22.962 -6.822 10.639 1 22.52 ? O_D LBV 328 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 43 #