data_5NWN # _model_server_result.job_id ihGx1avXf_PEqXENfWx2Zw _model_server_result.datetime_utc '2025-07-14 20:20:23' _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 5nwn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":600}' # _entry.id 5NWN # _exptl.entry_id 5NWN _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 4 _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 5NWN _cell.length_a 84.11 _cell.length_b 197.12 _cell.length_c 214.11 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NWN _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F 1 1 C,D,G,H 2 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 E N N ? 2 F N N ? 2 G N N ? 2 H 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 A SG CYS 38 A CYS 24 1_555 E CBA LBV . A LBV 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.603 ? covale ? covale2 B SG CYS 38 B CYS 24 1_555 F CBA LBV . B LBV 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.606 ? covale ? covale3 C SG CYS 38 C CYS 24 1_555 G CBA LBV . C LBV 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.601 ? covale ? covale4 D SG CYS 38 D CYS 24 1_555 H CBA LBV . D LBV 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.602 ? # _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 5NWN _atom_sites.fract_transf_matrix[1][1] 0.011889 _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] 0.005073 _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] 0.00467 _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 2 LBV A 1 600 600 LBV LBV . F 2 LBV B 1 600 600 LBV LBV . G 2 LBV C 1 600 600 LBV LBV . H 2 LBV D 1 600 600 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 . . . H 2 53.924 174.662 -42.741 1 241.66 ? C1A LBV 600 D 1 HETATM 2 C C1B LBV . . . H 2 54.979 178.911 -41.368 1 215.99 ? C1B LBV 600 D 1 HETATM 3 O O1B LBV . . . H 2 58.807 183.717 -39.522 1 208.73 ? O1B LBV 600 D 1 HETATM 4 C C1C LBV . . . H 2 56.016 180.695 -45.43 1 189.21 ? C1C LBV 600 D 1 HETATM 5 O O1C LBV . . . H 2 60.341 181.304 -47.085 1 174.12 ? O1C LBV 600 D 1 HETATM 6 C C1D LBV . . . H 2 55.559 177.591 -49.024 1 249.35 ? C1D LBV 600 D 1 HETATM 7 C C2A LBV . . . H 2 53.227 174.21 -41.438 1 247.02 ? C2A LBV 600 D 1 HETATM 8 C C2B LBV . . . H 2 55.386 180.018 -40.632 1 217.09 ? C2B LBV 600 D 1 HETATM 9 O O2B LBV . . . H 2 58.758 184.669 -41.501 1 205.17 ? O2B LBV 600 D 1 HETATM 10 C C2C LBV . . . H 2 56.454 181.369 -46.587 1 190.14 ? C2C LBV 600 D 1 HETATM 11 O O2C LBV . . . H 2 59.424 182.544 -48.619 1 200.53 ? O2C LBV 600 D 1 HETATM 12 C C2D LBV . . . H 2 54.867 176.696 -49.85 1 260.75 ? C2D LBV 600 D 1 HETATM 13 C C3A LBV . . . H 2 53.319 175.437 -40.656 1 250.08 ? C3A LBV 600 D 1 HETATM 14 C C3B LBV . . . H 2 55.835 180.961 -41.552 1 210.19 ? C3B LBV 600 D 1 HETATM 15 C C3C LBV . . . H 2 56.181 180.554 -47.696 1 197.65 ? C3C LBV 600 D 1 HETATM 16 C C3D LBV . . . H 2 55.697 176.405 -50.916 1 259.68 ? C3D LBV 600 D 1 HETATM 17 C C4A LBV . . . H 2 54.089 176.465 -41.29 1 241.27 ? C4A LBV 600 D 1 HETATM 18 C C4B LBV . . . H 2 55.704 180.412 -42.835 1 200.78 ? C4B LBV 600 D 1 HETATM 19 C C4C LBV . . . H 2 55.585 179.397 -47.169 1 208.49 ? C4C LBV 600 D 1 HETATM 20 C C4D LBV . . . H 2 56.865 177.123 -50.7 1 244.31 ? C4D LBV 600 D 1 HETATM 21 C CAA LBV . . . H 2 52.608 175.604 -39.476 1 256.3 ? CAA LBV 600 D 1 HETATM 22 C CAB LBV . . . H 2 56.383 182.321 -41.234 1 208.01 ? CAB LBV 600 D 1 HETATM 23 C CAC LBV . . . H 2 57.121 182.737 -46.651 1 193.48 ? CAC LBV 600 D 1 HETATM 24 C CAD LBV . . . H 2 55.336 175.468 -52.043 1 273.9 ? CAD LBV 600 D 1 HETATM 25 C CBA LBV . . . H 2 51.829 174.487 -38.847 1 259.04 ? CBA LBV 600 D 1 HETATM 26 C CBB LBV . . . H 2 57.89 182.434 -41.313 1 208.04 ? CBB LBV 600 D 1 HETATM 27 C CBC LBV . . . H 2 58.606 182.772 -46.391 1 195.34 ? CBC LBV 600 D 1 HETATM 28 C CBD LBV . . . H 2 55.982 175.437 -53.262 1 281 ? CBD LBV 600 D 1 HETATM 29 C CGB LBV . . . H 2 58.521 183.677 -40.752 1 207.58 ? CGB LBV 600 D 1 HETATM 30 C CGC LBV . . . H 2 59.504 182.177 -47.423 1 191.59 ? CGC LBV 600 D 1 HETATM 31 C CHB LBV . . . H 2 54.421 177.675 -40.673 1 229 ? CHB LBV 600 D 1 HETATM 32 C CHC LBV . . . H 2 56.112 181.174 -44.103 1 193.49 ? CHC LBV 600 D 1 HETATM 33 C CHD LBV . . . H 2 55.041 178.127 -47.84 1 233.6 ? CHD LBV 600 D 1 HETATM 34 C CMA LBV . . . H 2 54.024 173.118 -40.792 1 244.75 ? CMA LBV 600 D 1 HETATM 35 C CMB LBV . . . H 2 55.328 180.134 -39.138 1 218.5 ? CMB LBV 600 D 1 HETATM 36 C CMC LBV . . . H 2 56.492 180.918 -49.116 1 197.24 ? CMC LBV 600 D 1 HETATM 37 C CMD LBV . . . H 2 53.489 176.145 -49.653 1 263.8 ? CMD LBV 600 D 1 HETATM 38 N N_A LBV . . . H 2 54.441 176.052 -42.59 1 238.82 ? N_A LBV 600 D 1 HETATM 39 O O_A LBV . . . H 2 54.043 173.978 -43.751 1 240.05 ? O_A LBV 600 D 1 HETATM 40 N N_B LBV . . . H 2 55.18 179.167 -42.687 1 205.04 ? N_B LBV 600 D 1 HETATM 41 N N_C LBV . . . H 2 55.502 179.519 -45.83 1 190.64 ? N_C LBV 600 D 1 HETATM 42 N N_D LBV . . . H 2 56.766 177.823 -49.559 1 245 ? N_D LBV 600 D 1 HETATM 43 O O_D LBV . . . H 2 57.831 177.132 -51.406 1 234.42 ? O_D LBV 600 D 1 # _model_server_stats.io_time_ms 69 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 353 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 43 #