data_6SAW # _model_server_result.job_id Dy3GgLQn4sUVNERhP_zD7Q _model_server_result.datetime_utc '2024-11-07 19:47:56' _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 6saw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"W","auth_seq_id":401}' # _entry.id 6SAW # _exptl.entry_id 6SAW _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 8 _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 6SAW _cell.length_a 344.65 _cell.length_b 344.65 _cell.length_c 92.44 _cell.Z_PDB 72 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6SAW _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 software_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 PISA dimeric 2 software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,I,J,Y 1 1 C,M,N,AA 1 2 B,K,L,Z 2 1 E,Q,R,CA 2 2 D,G,O,P,U,V,BA,EA 3 1 F,H,S,T,W,X,DA,FA 4 1 # 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' 1_554 x,y,z-1 1 0 0 0 1 0 0 0 1 0 0 -92.44 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 I N N ? 2 K N N ? 2 M N N ? 2 O N N ? 2 Q N N ? 2 S N N ? 2 U N N ? 2 W 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 I CBA LBV . A LBV 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.875 ? covale ? covale2 B SG CYS 19 B CYS 17 1_555 K CBA LBV . B LBV 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.951 ? covale ? covale3 C SG CYS 19 C CYS 17 1_555 M CBA LBV . C LBV 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.741 ? covale ? covale4 D SG CYS 19 D CYS 17 1_555 O CBA LBV . D LBV 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.771 ? covale ? covale5 E SG CYS 19 E CYS 17 1_555 Q CBA LBV . E LBV 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.865 ? covale ? covale6 F SG CYS 19 F CYS 17 1_555 S CBA LBV . F LBV 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.911 ? covale ? covale7 G SG CYS 19 G CYS 17 1_555 U CBA LBV . G LBV 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.88 ? covale ? covale8 H SG CYS 19 H CYS 17 1_555 W CBA LBV . H LBV 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.895 ? # _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 6SAW _atom_sites.fract_transf_matrix[1][1] 0.002901 _atom_sites.fract_transf_matrix[1][2] 0.001675 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00335 _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] 0.010818 _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 I 2 LBV A 1 401 1 LBV LBV . J 3 CL A 1 402 1 CL CL . K 2 LBV B 1 401 2 LBV LBV . L 3 CL B 1 402 2 CL CL . M 2 LBV C 1 401 3 LBV LBV . N 3 CL C 1 402 3 CL CL . O 2 LBV D 1 401 4 LBV LBV . P 3 CL D 1 402 4 CL CL . Q 2 LBV E 1 401 5 LBV LBV . R 3 CL E 1 402 5 CL CL . S 2 LBV F 1 401 6 LBV LBV . T 3 CL F 1 402 6 CL CL . U 2 LBV G 1 401 7 LBV LBV . V 3 CL G 1 402 7 CL CL . W 2 LBV H 1 401 8 LBV LBV . X 3 CL H 1 402 8 CL CL . Y 4 HOH A 1 501 1 HOH HOH . Z 4 HOH B 1 501 2 HOH HOH . AA 4 HOH C 1 501 3 HOH HOH . BA 4 HOH D 1 501 4 HOH HOH . CA 4 HOH E 1 501 5 HOH HOH . DA 4 HOH F 1 501 6 HOH HOH . EA 4 HOH G 1 501 7 HOH HOH . FA 4 HOH H 1 501 8 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 . . . W 2 -57.129 50.399 102.125 1 77.09 ? C1A LBV 401 H 1 HETATM 2 C C1B LBV . . . W 2 -57.386 53.064 105.714 1 72.55 ? C1B LBV 401 H 1 HETATM 3 O O1B LBV . . . W 2 -57.548 58.059 108.791 1 61.66 ? O1B LBV 401 H 1 HETATM 4 C C1C LBV . . . W 2 -61.689 53.659 105.168 1 65.54 ? C1C LBV 401 H 1 HETATM 5 O O1C LBV . . . W 2 -63.994 57.032 105.205 1 75.76 ? O1C LBV 401 H 1 HETATM 6 C C1D LBV . . . W 2 -63.194 51.185 101.305 1 74.41 ? C1D LBV 401 H 1 HETATM 7 C C2A LBV . . . W 2 -56.093 49.582 102.628 1 75.74 ? C2A LBV 401 H 1 HETATM 8 C C2B LBV . . . W 2 -57.201 54.06 106.652 1 69.13 ? C2B LBV 401 H 1 HETATM 9 O O2B LBV . . . W 2 -59.422 58.924 107.956 1 62.15 ? O2B LBV 401 H 1 HETATM 10 C C2C LBV . . . W 2 -63.1 53.551 105.298 1 65.59 ? C2C LBV 401 H 1 HETATM 11 O O2C LBV . . . W 2 -64.98 55.665 103.736 1 69.53 ? O2C LBV 401 H 1 HETATM 12 C C2D LBV . . . W 2 -64.164 51.991 100.643 1 73.88 ? C2D LBV 401 H 1 HETATM 13 C C3A LBV . . . W 2 -55.699 50.178 103.878 1 75.33 ? C3A LBV 401 H 1 HETATM 14 C C3B LBV . . . W 2 -58.456 54.68 106.873 1 68.72 ? C3B LBV 401 H 1 HETATM 15 C C3C LBV . . . W 2 -63.555 52.742 104.25 1 73.33 ? C3C LBV 401 H 1 HETATM 16 C C3D LBV . . . W 2 -64.875 51.174 99.763 1 76.06 ? C3D LBV 401 H 1 HETATM 17 C C4A LBV . . . W 2 -56.485 51.321 104.076 1 70.9 ? C4A LBV 401 H 1 HETATM 18 C C4B LBV . . . W 2 -59.393 54.039 106.06 1 67.72 ? C4B LBV 401 H 1 HETATM 19 C C4C LBV . . . W 2 -62.41 52.377 103.472 1 74.09 ? C4C LBV 401 H 1 HETATM 20 C C4D LBV . . . W 2 -64.368 49.872 99.859 1 76.93 ? C4D LBV 401 H 1 HETATM 21 C CAA LBV . . . W 2 -54.716 49.739 104.775 1 82.63 ? CAA LBV 401 H 1 HETATM 22 C CAB LBV . . . W 2 -58.746 55.759 107.766 1 69.25 ? CAB LBV 401 H 1 HETATM 23 C CAC LBV . . . W 2 -63.839 54.169 106.357 1 67.4 ? CAC LBV 401 H 1 HETATM 24 C CAD LBV . . . W 2 -65.943 51.452 98.864 1 75.33 ? CAD LBV 401 H 1 HETATM 25 C CBA LBV . . . W 2 -53.91 48.587 104.611 1 92.77 ? CBA LBV 401 H 1 HETATM 26 C CBB LBV . . . W 2 -58.637 57.001 107.076 1 67.54 ? CBB LBV 401 H 1 HETATM 27 C CBC LBV . . . W 2 -64.923 55.058 105.929 1 72.44 ? CBC LBV 401 H 1 HETATM 28 C CBD LBV . . . W 2 -66.515 52.694 98.688 1 74.94 ? CBD LBV 401 H 1 HETATM 29 C CGB LBV . . . W 2 -58.524 58.078 108.022 1 65.64 ? CGB LBV 401 H 1 HETATM 30 C CGC LBV . . . W 2 -64.589 55.981 104.868 1 75.71 ? CGC LBV 401 H 1 HETATM 31 C CHB LBV . . . W 2 -56.424 52.181 105.161 1 71.58 ? CHB LBV 401 H 1 HETATM 32 C CHC LBV . . . W 2 -60.752 54.316 105.941 1 64.61 ? CHC LBV 401 H 1 HETATM 33 C CHD LBV . . . W 2 -62.271 51.59 102.279 1 72.73 ? CHD LBV 401 H 1 HETATM 34 C CMA LBV . . . W 2 -55.085 49.647 101.64 1 79.33 ? CMA LBV 401 H 1 HETATM 35 C CMB LBV . . . W 2 -55.981 54.401 107.264 1 68.96 ? CMB LBV 401 H 1 HETATM 36 C CMC LBV . . . W 2 -64.891 52.347 103.99 1 73.64 ? CMC LBV 401 H 1 HETATM 37 C CMD LBV . . . W 2 -64.282 53.384 100.902 1 69.64 ? CMD LBV 401 H 1 HETATM 38 N N_A LBV . . . W 2 -57.315 51.426 103.016 1 75.41 ? N_A LBV 401 H 1 HETATM 39 O O_A LBV . . . W 2 -57.782 50.29 101.063 1 69.57 ? O_A LBV 401 H 1 HETATM 40 N N_B LBV . . . W 2 -58.71 53.059 105.372 1 69.92 ? N_B LBV 401 H 1 HETATM 41 N N_C LBV . . . W 2 -61.333 52.944 104.066 1 71.04 ? N_C LBV 401 H 1 HETATM 42 N N_D LBV . . . W 2 -63.365 49.921 100.793 1 74.1 ? N_D LBV 401 H 1 HETATM 43 O O_D LBV . . . W 2 -64.664 48.815 99.287 1 78.04 ? O_D LBV 401 H 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 32 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 43 #