data_5LLX # _model_server_result.job_id 1nPd8hIZ61Sn5_AQzWkMmA _model_server_result.datetime_utc '2024-12-01 06:51:31' _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 5llx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":701}' # _entry.id 5LLX # _exptl.entry_id 5LLX _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 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 5LLX _cell.length_a 50.73 _cell.length_b 78.64 _cell.length_c 452.04 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LLX _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 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,E,F,G,H,I,J,K,L _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 G 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 19 A CYS 17 1_555 C CBA LBV . A LBV 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.777 ? covale ? covale2 B SG CYS 19 B CYS 17 1_555 G CBA LBV . B LBV 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.663 ? metalc ? metalc1 A OD1 ASP 566 A ASP 564 1_555 F MG MG . A MG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? metalc ? metalc2 A O LEU 567 A LEU 565 1_555 F MG MG . A MG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc3 A OE2 GLU 609 A GLU 607 1_555 F MG MG . A MG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.786 ? metalc ? metalc4 E O1G GTP . A GTP 703 1_555 F MG MG . A MG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc5 E O1B GTP . A GTP 703 1_555 F MG MG . A MG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? metalc ? metalc6 E O1A GTP . A GTP 703 1_555 F MG MG . A MG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? metalc ? metalc7 B OD1 ASP 566 B ASP 564 1_555 J MG MG . B MG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.91 ? metalc ? metalc8 B O LEU 567 B LEU 565 1_555 J MG MG . B MG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.212 ? metalc ? metalc9 B OE2 GLU 609 B GLU 607 1_555 J MG MG . B MG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.848 ? metalc ? metalc10 I O1G GTP . B GTP 703 1_555 J MG MG . B MG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc11 I O1B GTP . B GTP 703 1_555 J MG MG . B MG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.881 ? metalc ? metalc12 I O1A GTP . B GTP 703 1_555 J MG MG . B MG 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.489 ? # _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 223 n n C1A C2A LBV sing 224 n n C1B C2B LBV doub 225 n y C1B CHB LBV sing 226 n n O1B CGB LBV doub 227 n n C1C CHC LBV doub 228 z n C1D CHD LBV doub 229 z n C2A CMA LBV sing 230 n n C2A C3A LBV sing 231 n n C2B CMB LBV sing 232 n n C2C C1C LBV sing 233 n n O2C CGC LBV doub 234 n n C2D C1D LBV sing 235 n n C2D CMD LBV sing 236 n n C3A CAA LBV doub 237 e n C3B C2B LBV sing 238 n y C3B CAB LBV sing 239 n n C3C C2C LBV doub 240 n n C3C C4C LBV sing 241 n n C3D C2D LBV doub 242 n n C4A C3A LBV sing 243 n n C4A CHB LBV doub 244 z n C4B C3B LBV doub 245 n y C4B N_B LBV sing 246 n y C4C N_C LBV doub 247 n n C4D C3D LBV sing 248 n n C4D N_D LBV sing 249 n n CAA CBA LBV sing 250 n n CAC C2C LBV sing 251 n n CAC CBC LBV sing 252 n n CAD C3D LBV sing 253 n n CBB CAB LBV sing 254 n n CBB CGB LBV sing 255 n n CBD CAD LBV doub 256 n n CGB O2B LBV sing 257 n n CGC O1C LBV sing 258 n n CGC CBC LBV sing 259 n n CHC C4B LBV sing 260 n n CHD C4C LBV sing 261 n n CMC C3C LBV sing 262 n n N_A C4A LBV sing 263 n n O_A C1A LBV doub 264 n n N_B C1B LBV sing 265 n y N_C C1C LBV sing 266 n n N_D C1D LBV sing 267 n n O_D C4D LBV doub 268 n n O1C HO1C LBV sing 269 n n C2A H2A LBV sing 270 n n O2B HO2B LBV sing 271 n n CAA HAA1 LBV sing 272 n n CAB HAB1 LBV sing 273 n n CAB HAB2 LBV sing 274 n n CAC HAC1 LBV sing 275 n n CAC HAC2 LBV sing 276 n n CAD HAD1 LBV sing 277 n n CBA HBA1 LBV sing 278 n n CBA HBA2 LBV sing 279 n n CBA HBA3 LBV sing 280 n n CBB HBB1 LBV sing 281 n n CBB HBB2 LBV sing 282 n n CBC HBC1 LBV sing 283 n n CBC HBC2 LBV sing 284 n n CBD HBD1 LBV sing 285 n n CBD HBD2 LBV sing 286 n n CHB HHB1 LBV sing 287 n n CHC HHC1 LBV sing 288 n n CHD HHD1 LBV sing 289 n n CMA HMA1 LBV sing 290 n n CMA HMA2 LBV sing 291 n n CMA HMA3 LBV sing 292 n n CMB HMB1 LBV sing 293 n n CMB HMB2 LBV sing 294 n n CMB HMB3 LBV sing 295 n n CMC HMC1 LBV sing 296 n n CMC HMC2 LBV sing 297 n n CMC HMC3 LBV sing 298 n n CMD HMD1 LBV sing 299 n n CMD HMD2 LBV sing 300 n n CMD HMD3 LBV sing 301 n n N_A HAD LBV sing 302 n n N_B HAE LBV sing 303 n n N_C HAF LBV sing 304 n n N_D HAG LBV sing 305 n n # _atom_sites.entry_id 5LLX _atom_sites.fract_transf_matrix[1][1] 0.019712 _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] 0.012716 _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] 0.002212 _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 1 701 2 LBV LBV . D 3 CL A 1 702 2 CL CL . E 4 GTP A 1 703 2 GTP GTP . F 5 MG A 1 704 1 MG MG . G 2 LBV B 1 701 1 LBV LBV . H 3 CL B 1 702 1 CL CL . I 4 GTP B 1 703 1 GTP GTP . J 5 MG B 1 704 2 MG MG . K 6 HOH A 1 801 11 HOH HOH . K 6 HOH A 2 802 3 HOH HOH . L 6 HOH B 1 801 10 HOH HOH . L 6 HOH B 2 802 9 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 . . . C 2 29.397 44.834 493.876 1 76.97 ? C1A LBV 701 A 1 HETATM 2 C C1B LBV . . . C 2 25.612 45.159 491.348 1 89.07 ? C1B LBV 701 A 1 HETATM 3 O O1B LBV . . . C 2 21.182 45.802 487.174 1 84.02 ? O1B LBV 701 A 1 HETATM 4 C C1C LBV . . . C 2 25.37 41.097 489.101 1 72.63 ? C1C LBV 701 A 1 HETATM 5 O O1C LBV . . . C 2 26.285 39.68 485.432 1 99.75 ? O1C LBV 701 A 1 HETATM 6 C C1D LBV . . . C 2 28.469 37.55 489.816 1 83.94 ? C1D LBV 701 A 1 HETATM 7 C C2A LBV . . . C 2 29.143 46.014 494.622 1 84.99 ? C2A LBV 701 A 1 HETATM 8 C C2B LBV . . . C 2 24.446 45.57 490.753 1 93.05 ? C2B LBV 701 A 1 HETATM 9 O O2B LBV . . . C 2 22.256 44.294 485.976 1 74.82 ? O2B LBV 701 A 1 HETATM 10 C C2C LBV . . . C 2 24.964 39.985 488.309 1 73.01 ? C2C LBV 701 A 1 HETATM 11 O O2C LBV . . . C 2 24.385 38.791 484.721 1 110.1 ? O2C LBV 701 A 1 HETATM 12 C C2D LBV . . . C 2 29.089 36.603 490.645 1 90.59 ? C2D LBV 701 A 1 HETATM 13 C C3A LBV . . . C 2 27.814 46.4 494.269 1 81.16 ? C3A LBV 701 A 1 HETATM 14 C C3B LBV . . . C 2 24.04 44.576 489.86 1 86.24 ? C3B LBV 701 A 1 HETATM 15 C C3C LBV . . . C 2 25.766 38.917 488.614 1 71.45 ? C3C LBV 701 A 1 HETATM 16 C C3D LBV . . . C 2 29.722 35.674 489.845 1 96.05 ? C3D LBV 701 A 1 HETATM 17 C C4A LBV . . . C 2 27.46 45.668 493.114 1 81.9 ? C4A LBV 701 A 1 HETATM 18 C C4B LBV . . . C 2 24.953 43.541 489.9 1 76.94 ? C4B LBV 701 A 1 HETATM 19 C C4C LBV . . . C 2 26.695 39.348 489.594 1 67.92 ? C4C LBV 701 A 1 HETATM 20 C C4D LBV . . . C 2 29.5 36.035 488.491 1 91.77 ? C4D LBV 701 A 1 HETATM 21 C CAA LBV . . . C 2 27.069 47.462 494.809 1 73.86 ? CAA LBV 701 A 1 HETATM 22 C CAB LBV . . . C 2 22.891 44.584 489.035 1 79.96 ? CAB LBV 701 A 1 HETATM 23 C CAC LBV . . . C 2 23.888 39.996 487.372 1 80.29 ? CAC LBV 701 A 1 HETATM 24 C CAD LBV . . . C 2 30.478 34.535 490.226 1 92.32 ? CAD LBV 701 A 1 HETATM 25 C CBA LBV . . . C 2 27.434 48.186 495.984 1 64.22 ? CBA LBV 701 A 1 HETATM 26 C CBB LBV . . . C 2 23.254 45.145 487.783 1 76.87 ? CBB LBV 701 A 1 HETATM 27 C CBC LBV . . . C 2 24.323 40.563 486.131 1 88.47 ? CBC LBV 701 A 1 HETATM 28 C CBD LBV . . . C 2 31.101 33.705 489.31 1 89.11 ? CBD LBV 701 A 1 HETATM 29 C CGB LBV . . . C 2 22.14 45.079 486.909 1 77.46 ? CGB LBV 701 A 1 HETATM 30 C CGC LBV . . . C 2 25.052 39.599 485.368 1 103.74 ? CGC LBV 701 A 1 HETATM 31 C CHB LBV . . . C 2 26.348 45.897 492.322 1 93.74 ? CHB LBV 701 A 1 HETATM 32 C CHC LBV . . . C 2 24.837 42.388 489.108 1 77.62 ? CHC LBV 701 A 1 HETATM 33 C CHD LBV . . . C 2 27.735 38.638 490.235 1 65.93 ? CHD LBV 701 A 1 HETATM 34 C CMA LBV . . . C 2 30.12 46.963 494.236 1 83.22 ? CMA LBV 701 A 1 HETATM 35 C CMB LBV . . . C 2 23.774 46.787 491.006 1 85.4 ? CMB LBV 701 A 1 HETATM 36 C CMC LBV . . . C 2 25.667 37.623 488.044 1 61.75 ? CMC LBV 701 A 1 HETATM 37 C CMD LBV . . . C 2 29.008 36.692 492.052 1 84.64 ? CMD LBV 701 A 1 HETATM 38 N N_A LBV . . . C 2 28.421 44.734 492.925 1 72.6 ? N_A LBV 701 A 1 HETATM 39 O O_A LBV . . . C 2 30.417 44.141 493.841 1 75.08 ? O_A LBV 701 A 1 HETATM 40 N N_B LBV . . . C 2 25.93 43.913 490.824 1 73.09 ? N_B LBV 701 A 1 HETATM 41 N N_C LBV . . . C 2 26.428 40.666 489.86 1 70.04 ? N_C LBV 701 A 1 HETATM 42 N N_D LBV . . . C 2 28.745 37.167 488.533 1 89.54 ? N_D LBV 701 A 1 HETATM 43 O O_D LBV . . . C 2 29.836 35.559 487.405 1 80.19 ? O_D LBV 701 A 1 # _model_server_stats.io_time_ms 106 _model_server_stats.parse_time_ms 36 _model_server_stats.create_model_time_ms 58 _model_server_stats.query_time_ms 808 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 43 #