data_8U4X # _model_server_result.job_id ALuMiZzp9LMdwD7XMYAKhw _model_server_result.datetime_utc '2024-11-15 08:34:09' _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 8u4x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":900}' # _entry.id 8U4X # _exptl.entry_id 8U4X _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _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 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 8U4X _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8U4X _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 2 C N N ? 2 D 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 disulf ? disulf1 A SG CYS 376 A CYS 375 1_555 A SG CYS 380 A CYS 379 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 B SG CYS 376 B CYS 375 1_555 B SG CYS 380 B CYS 379 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A SG CYS 17 A CYS 16 1_555 C CBA LBV . A LBV 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.7 ? covale ? covale2 B SG CYS 17 B CYS 16 1_555 D CBA LBV . B LBV 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.7 ? # _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 171 n n C1A C2A LBV sing 172 n n C1B C2B LBV doub 173 n y C1B CHB LBV sing 174 n n O1B CGB LBV doub 175 n n C1C CHC LBV doub 176 z n C1D CHD LBV doub 177 z n C2A CMA LBV sing 178 n n C2A C3A LBV sing 179 n n C2B CMB LBV sing 180 n n C2C C1C LBV sing 181 n n O2C CGC LBV doub 182 n n C2D C1D LBV sing 183 n n C2D CMD LBV sing 184 n n C3A CAA LBV doub 185 e n C3B C2B LBV sing 186 n y C3B CAB LBV sing 187 n n C3C C2C LBV doub 188 n n C3C C4C LBV sing 189 n n C3D C2D LBV doub 190 n n C4A C3A LBV sing 191 n n C4A CHB LBV doub 192 z n C4B C3B LBV doub 193 n y C4B N_B LBV sing 194 n y C4C N_C LBV doub 195 n n C4D C3D LBV sing 196 n n C4D N_D LBV sing 197 n n CAA CBA LBV sing 198 n n CAC C2C LBV sing 199 n n CAC CBC LBV sing 200 n n CAD C3D LBV sing 201 n n CBB CAB LBV sing 202 n n CBB CGB LBV sing 203 n n CBD CAD LBV doub 204 n n CGB O2B LBV sing 205 n n CGC O1C LBV sing 206 n n CGC CBC LBV sing 207 n n CHC C4B LBV sing 208 n n CHD C4C LBV sing 209 n n CMC C3C LBV sing 210 n n N_A C4A LBV sing 211 n n O_A C1A LBV doub 212 n n N_B C1B LBV sing 213 n y N_C C1C LBV sing 214 n n N_D C1D LBV sing 215 n n O_D C4D LBV doub 216 n n O1C HO1C LBV sing 217 n n C2A H2A LBV sing 218 n n O2B HO2B LBV sing 219 n n CAA HAA1 LBV sing 220 n n CAB HAB1 LBV sing 221 n n CAB HAB2 LBV sing 222 n n CAC HAC1 LBV sing 223 n n CAC HAC2 LBV sing 224 n n CAD HAD1 LBV sing 225 n n CBA HBA1 LBV sing 226 n n CBA HBA2 LBV sing 227 n n CBA HBA3 LBV sing 228 n n CBB HBB1 LBV sing 229 n n CBB HBB2 LBV sing 230 n n CBC HBC1 LBV sing 231 n n CBC HBC2 LBV sing 232 n n CBD HBD1 LBV sing 233 n n CBD HBD2 LBV sing 234 n n CHB HHB1 LBV sing 235 n n CHC HHC1 LBV sing 236 n n CHD HHD1 LBV sing 237 n n CMA HMA1 LBV sing 238 n n CMA HMA2 LBV sing 239 n n CMA HMA3 LBV sing 240 n n CMB HMB1 LBV sing 241 n n CMB HMB2 LBV sing 242 n n CMB HMB3 LBV sing 243 n n CMC HMC1 LBV sing 244 n n CMC HMC2 LBV sing 245 n n CMC HMC3 LBV sing 246 n n CMD HMD1 LBV sing 247 n n CMD HMD2 LBV sing 248 n n CMD HMD3 LBV sing 249 n n N_A HAD LBV sing 250 n n N_B HAE LBV sing 251 n n N_C HAF LBV sing 252 n n N_D HAG LBV sing 253 n n # _atom_sites.entry_id 8U4X _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 C 2 LBV A 1 900 900 LBV LBV . D 2 LBV B 1 900 900 LBV LBV . # 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 . . . C 2 160.541 117.142 125.433 1 57.55 ? C1A LBV 900 A 1 HETATM 2 C C1B LBV . . . C 2 160.172 121.477 124.512 1 56.4 ? C1B LBV 900 A 1 HETATM 3 O O1B LBV . . . C 2 157.924 126.756 121.506 1 54.33 ? O1B LBV 900 A 1 HETATM 4 C C1C LBV . . . C 2 155.994 121.263 122.923 1 53.47 ? C1C LBV 900 A 1 HETATM 5 O O1C LBV . . . C 2 152.461 122.676 119.183 1 58.18 ? O1C LBV 900 A 1 HETATM 6 C C1D LBV . . . C 2 153.462 117.342 123.418 1 53.39 ? C1D LBV 900 A 1 HETATM 7 C C2A LBV . . . C 2 161.964 117.147 125.937 1 53.67 ? C2A LBV 900 A 1 HETATM 8 C C2B LBV . . . C 2 160.265 122.88 124.301 1 55.03 ? C2B LBV 900 A 1 HETATM 9 O O2B LBV . . . C 2 159.955 126.957 120.609 1 59.8 ? O2B LBV 900 A 1 HETATM 10 C C2C LBV . . . C 2 154.678 121.579 122.563 1 53.5 ? C2C LBV 900 A 1 HETATM 11 O O2C LBV . . . C 2 153.686 120.829 119.421 1 60.37 ? O2C LBV 900 A 1 HETATM 12 C C2D LBV . . . C 2 152.719 116.33 124.154 1 51.68 ? C2D LBV 900 A 1 HETATM 13 C C3A LBV . . . C 2 162.294 118.614 125.991 1 57.13 ? C3A LBV 900 A 1 HETATM 14 C C3B LBV . . . C 2 159.14 123.274 123.62 1 54.74 ? C3B LBV 900 A 1 HETATM 15 C C3C LBV . . . C 2 153.871 120.486 122.895 1 54.99 ? C3C LBV 900 A 1 HETATM 16 C C3D LBV . . . C 2 151.929 115.656 123.28 1 51.58 ? C3D LBV 900 A 1 HETATM 17 C C4A LBV . . . C 2 161.247 119.333 125.265 1 59.09 ? C4A LBV 900 A 1 HETATM 18 C C4B LBV . . . C 2 158.329 122.117 123.405 1 54.11 ? C4B LBV 900 A 1 HETATM 19 C C4C LBV . . . C 2 154.704 119.508 123.451 1 53.93 ? C4C LBV 900 A 1 HETATM 20 C C4D LBV . . . C 2 152.15 116.23 121.93 1 50.19 ? C4D LBV 900 A 1 HETATM 21 C CAA LBV . . . C 2 163.2 119.214 126.77 1 64.19 ? CAA LBV 900 A 1 HETATM 22 C CAB LBV . . . C 2 158.795 124.652 123.179 1 53.92 ? CAB LBV 900 A 1 HETATM 23 C CAC LBV . . . C 2 154.21 122.851 121.946 1 52.45 ? CAC LBV 900 A 1 HETATM 24 C CAD LBV . . . C 2 151.025 114.568 123.587 1 56.42 ? CAD LBV 900 A 1 HETATM 25 C CBA LBV . . . C 2 163.54 118.858 128.172 1 71.07 ? CBA LBV 900 A 1 HETATM 26 C CBB LBV . . . C 2 159.521 125.02 121.886 1 51.12 ? CBB LBV 900 A 1 HETATM 27 C CBC LBV . . . C 2 154.456 122.852 120.436 1 54.83 ? CBC LBV 900 A 1 HETATM 28 C CBD LBV . . . C 2 150.469 113.712 122.724 1 55.27 ? CBD LBV 900 A 1 HETATM 29 C CGB LBV . . . C 2 159.085 126.366 121.28 1 53.61 ? CGB LBV 900 A 1 HETATM 30 C CGC LBV . . . C 2 153.447 122.038 119.604 1 60.04 ? CGC LBV 900 A 1 HETATM 31 C CHB LBV . . . C 2 161.139 120.687 125.183 1 60.63 ? CHB LBV 900 A 1 HETATM 32 C CHC LBV . . . C 2 157.12 122.082 122.755 1 54.81 ? CHC LBV 900 A 1 HETATM 33 C CHD LBV . . . C 2 154.352 118.213 123.943 1 54.73 ? CHD LBV 900 A 1 HETATM 34 C CMA LBV . . . C 2 162.845 116.352 124.973 1 56.43 ? CMA LBV 900 A 1 HETATM 35 C CMB LBV . . . C 2 161.408 123.717 124.76 1 60.51 ? CMB LBV 900 A 1 HETATM 36 C CMC LBV . . . C 2 152.397 120.427 122.677 1 57.22 ? CMC LBV 900 A 1 HETATM 37 C CMD LBV . . . C 2 152.864 116.139 125.621 1 53.57 ? CMD LBV 900 A 1 HETATM 38 N N_A LBV . . . C 2 160.223 118.439 125.07 1 57.11 ? N_A LBV 900 A 1 HETATM 39 O O_A LBV . . . C 2 159.785 116.21 125.342 1 63.1 ? O_A LBV 900 A 1 HETATM 40 N N_B LBV . . . C 2 159.013 121.053 123.969 1 55.92 ? N_B LBV 900 A 1 HETATM 41 N N_C LBV . . . C 2 155.988 119.987 123.461 1 53.34 ? N_C LBV 900 A 1 HETATM 42 N N_D LBV . . . C 2 153.08 117.233 122.093 1 55.41 ? N_D LBV 900 A 1 HETATM 43 O O_D LBV . . . C 2 151.649 115.926 120.868 1 54.11 ? O_D LBV 900 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 1022 _model_server_stats.encode_time_ms 18 _model_server_stats.element_count 43 #