data_5MG1 # _model_server_result.job_id sgC-bzsHX6iVLl0MuXi1RA _model_server_result.datetime_utc '2024-11-08 05:46:15' _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 5mg1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 5MG1 # _exptl.entry_id 5MG1 _exptl.method 'X-RAY DIFFRACTION' # _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 1 _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 120 _cell.entry_id 5MG1 _cell.length_a 151.7 _cell.length_b 151.7 _cell.length_c 151.2 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5MG1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details software_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' 11_555 -x+y,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 601 _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 1.703 _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 5MG1 _atom_sites.fract_transf_matrix[1][1] 0.006592 _atom_sites.fract_transf_matrix[1][2] 0.003806 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007612 _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] 0.006614 _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 1 601 550 LBV LBV . C 3 HOH A 1 701 8 HOH HOH . C 3 HOH A 2 702 1 HOH HOH . C 3 HOH A 3 703 5 HOH HOH . C 3 HOH A 4 704 4 HOH HOH . C 3 HOH A 5 705 3 HOH HOH . C 3 HOH A 6 706 2 HOH HOH . C 3 HOH A 7 707 7 HOH HOH . C 3 HOH A 8 708 6 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 -24.623 61.909 17.648 1 70.84 ? C1A LBV 601 A 1 HETATM 2 C C1B LBV . . . B 2 -20.565 60.515 18.922 1 70.28 ? C1B LBV 601 A 1 HETATM 3 O O1B LBV . . . B 2 -15.509 56.183 19.832 1 82.23 ? O1B LBV 601 A 1 HETATM 4 C C1C LBV . . . B 2 -19.256 59.099 14.877 1 71.2 ? C1C LBV 601 A 1 HETATM 5 O O1C LBV . . . B 2 -17.384 55.574 11.897 1 50.91 ? O1C LBV 601 A 1 HETATM 6 C C1D LBV . . . B 2 -22.156 59.552 11.157 1 74.67 ? C1D LBV 601 A 1 HETATM 7 C C2A LBV . . . B 2 -24.914 62.815 18.826 1 66.07 ? C2A LBV 601 A 1 HETATM 8 C C2B LBV . . . B 2 -19.473 59.977 19.599 1 78.47 ? C2B LBV 601 A 1 HETATM 9 O O2B LBV . . . B 2 -15.607 55.952 17.662 1 87.96 ? O2B LBV 601 A 1 HETATM 10 C C2C LBV . . . B 2 -18.595 58.513 13.727 1 65.11 ? C2C LBV 601 A 1 HETATM 11 O O2C LBV . . . B 2 -18.848 54.57 13.163 1 80.79 ? O2C LBV 601 A 1 HETATM 12 C C2D LBV . . . B 2 -22.907 60.332 10.182 1 71.52 ? C2D LBV 601 A 1 HETATM 13 C C3A LBV . . . B 2 -23.714 62.58 19.629 1 74.46 ? C3A LBV 601 A 1 HETATM 14 C C3B LBV . . . B 2 -18.665 59.345 18.659 1 68.85 ? C3B LBV 601 A 1 HETATM 15 C C3C LBV . . . B 2 -19.351 58.792 12.637 1 60.86 ? C3C LBV 601 A 1 HETATM 16 C C3D LBV . . . B 2 -23.31 59.459 9.193 1 67.47 ? C3D LBV 601 A 1 HETATM 17 C C4A LBV . . . B 2 -22.829 61.66 18.991 1 78.35 ? C4A LBV 601 A 1 HETATM 18 C C4B LBV . . . B 2 -19.271 59.511 17.41 1 61.99 ? C4B LBV 601 A 1 HETATM 19 C C4C LBV . . . B 2 -20.514 59.543 13.084 1 70.98 ? C4C LBV 601 A 1 HETATM 20 C C4D LBV . . . B 2 -22.799 58.122 9.57 1 74.58 ? C4D LBV 601 A 1 HETATM 21 C CAA LBV . . . B 2 -23.408 63.14 20.81 1 78.26 ? CAA LBV 601 A 1 HETATM 22 C CAB LBV . . . B 2 -17.367 58.621 18.925 1 63.41 ? CAB LBV 601 A 1 HETATM 23 C CAC LBV . . . B 2 -17.285 57.738 13.715 1 68.98 ? CAC LBV 601 A 1 HETATM 24 C CAD LBV . . . B 2 -24.12 59.729 7.936 1 57.63 ? CAD LBV 601 A 1 HETATM 25 C CBA LBV . . . B 2 -24.256 64.124 21.558 1 79.22 ? CBA LBV 601 A 1 HETATM 26 C CBB LBV . . . B 2 -17.428 57.117 18.726 1 64.82 ? CBB LBV 601 A 1 HETATM 27 C CBC LBV . . . B 2 -17.416 56.286 14.103 1 76.68 ? CBC LBV 601 A 1 HETATM 28 C CBD LBV . . . B 2 -24.38 58.522 7.071 1 54.17 ? CBD LBV 601 A 1 HETATM 29 C CGB LBV . . . B 2 -16.111 56.375 18.74 1 77.52 ? CGB LBV 601 A 1 HETATM 30 C CGC LBV . . . B 2 -17.933 55.412 13.012 1 71.23 ? CGC LBV 601 A 1 HETATM 31 C CHB LBV . . . B 2 -21.607 61.238 19.529 1 78.12 ? CHB LBV 601 A 1 HETATM 32 C CHC LBV . . . B 2 -18.758 59.005 16.199 1 64.63 ? CHC LBV 601 A 1 HETATM 33 C CHD LBV . . . B 2 -21.573 60.078 12.328 1 78.92 ? CHD LBV 601 A 1 HETATM 34 C CMA LBV . . . B 2 -26.166 62.298 19.455 1 65.05 ? CMA LBV 601 A 1 HETATM 35 C CMB LBV . . . B 2 -19.246 60.079 21.074 1 91.23 ? CMB LBV 601 A 1 HETATM 36 C CMC LBV . . . B 2 -19.06 58.4 11.228 1 54.66 ? CMC LBV 601 A 1 HETATM 37 C CMD LBV . . . B 2 -23.188 61.798 10.23 1 76.39 ? CMD LBV 601 A 1 HETATM 38 N N_A LBV . . . B 2 -23.417 61.256 17.779 1 74.5 ? N_A LBV 601 A 1 HETATM 39 O O_A LBV . . . B 2 -25.382 61.77 16.693 1 75.77 ? O_A LBV 601 A 1 HETATM 40 N N_B LBV . . . B 2 -20.423 60.219 17.595 1 62.75 ? N_B LBV 601 A 1 HETATM 41 N N_C LBV . . . B 2 -20.392 59.697 14.438 1 78.05 ? N_C LBV 601 A 1 HETATM 42 N N_D LBV . . . B 2 -22.134 58.266 10.742 1 73.31 ? N_D LBV 601 A 1 HETATM 43 O O_D LBV . . . B 2 -22.923 57.062 8.984 1 77.34 ? O_D LBV 601 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 43 #