data_5U6G # _model_server_result.job_id nw-dE7DUlwAvua-EAqhfxg _model_server_result.datetime_utc '2024-11-26 01:06:59' _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 5u6g # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"S","auth_seq_id":201}' # _entry.id 5U6G # _exptl.entry_id 5U6G _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 284.436 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description RETINAL _entity.pdbx_number_of_molecules 11 _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 5U6G _cell.length_a 65.474 _cell.length_b 73.597 _cell.length_c 351.601 _cell.Z_PDB 40 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5U6G _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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 PISA dimeric 2 author_and_software_defined_assembly 4 PISA dimeric 2 author_and_software_defined_assembly 5 PISA dimeric 2 author_and_software_defined_assembly 6 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,G,M,S,X,DA 1 1 B,F,N,R,Y,CA 2 1 C,H,O,T,Z,EA 3 1 D,E,P,Q,AA,BA 4 1 I,K,U,V,FA,HA 5 1 J,L,W,GA,IA 6 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 ? 3 M N N ? 3 N N N ? 3 O N N ? 3 P N N ? 3 Q N N ? 3 R N N ? 3 S N N ? 3 T N N ? 3 U N N ? 3 V N N ? 3 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 NZ LYS 108 A LYS 108 1_555 M C15 RET . A RET 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.437 ? covale ? covale2 C NZ LYS 108 C LYS 108 1_555 O C15 RET . C RET 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.562 ? covale ? covale3 E NZ LYS 108 H LYS 108 1_555 Q C15 RET . H RET 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.3 ? covale ? covale4 F NZ LYS 108 E LYS 108 1_555 R C15 RET . E RET 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale5 I NZ LYS 108 I LYS 108 1_555 U C15 RET . I RET 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.473 ? covale ? covale6 K NZ LYS 108 K LYS 108 1_555 V C15 RET . K RET 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.379 ? # _chem_comp.formula 'C20 H28 O' _chem_comp.formula_weight 284.436 _chem_comp.id RET _chem_comp.mon_nstd_flag . _chem_comp.name RETINAL _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 C1 C2 RET sing 260 n n C1 C6 RET sing 261 n n C1 C16 RET sing 262 n n C1 C17 RET sing 263 n n C2 C3 RET sing 264 n n C2 H21 RET sing 265 n n C2 H22 RET sing 266 n n C3 C4 RET sing 267 n n C3 H31 RET sing 268 n n C3 H32 RET sing 269 n n C4 C5 RET sing 270 n n C4 H41 RET sing 271 n n C4 H42 RET sing 272 n n C5 C6 RET doub 273 n n C5 C18 RET sing 274 n n C6 C7 RET sing 275 n n C7 C8 RET doub 276 e n C7 H7 RET sing 277 n n C8 C9 RET sing 278 n n C8 H8 RET sing 279 n n C9 C10 RET doub 280 e n C9 C19 RET sing 281 n n C10 C11 RET sing 282 n n C10 H10 RET sing 283 n n C11 C12 RET doub 284 e n C11 H11 RET sing 285 n n C12 C13 RET sing 286 n n C12 H12 RET sing 287 n n C13 C14 RET doub 288 e n C13 C20 RET sing 289 n n C14 C15 RET sing 290 n n C14 H14 RET sing 291 n n C15 O1 RET doub 292 n n C15 H15 RET sing 293 n n C16 H161 RET sing 294 n n C16 H162 RET sing 295 n n C16 H163 RET sing 296 n n C17 H171 RET sing 297 n n C17 H172 RET sing 298 n n C17 H173 RET sing 299 n n C18 H181 RET sing 300 n n C18 H182 RET sing 301 n n C18 H183 RET sing 302 n n C19 H191 RET sing 303 n n C19 H192 RET sing 304 n n C19 H193 RET sing 305 n n C20 H201 RET sing 306 n n C20 H202 RET sing 307 n n C20 H203 RET sing 308 n n # _atom_sites.entry_id 5U6G _atom_sites.fract_transf_matrix[1][1] 0.015273 _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] 0.013588 _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] 0.002844 _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 M 3 RET A 1 201 5 RET RET . N 3 RET B 1 201 7 RET RET . O 3 RET C 1 201 9 RET RET . P 3 RET D 1 201 1 RET RET . Q 3 RET H 1 201 10 RET RET . R 3 RET E 1 201 3 RET RET . S 3 RET F 1 201 4 RET RET . T 3 RET G 1 201 2 RET RET . U 3 RET I 1 201 8 RET RET . V 3 RET K 1 201 11 RET RET . W 3 RET L 1 201 6 RET RET . X 4 HOH A 1 301 46 HOH HOH . X 4 HOH A 2 302 140 HOH HOH . X 4 HOH A 3 303 199 HOH HOH . X 4 HOH A 4 304 49 HOH HOH . X 4 HOH A 5 305 45 HOH HOH . X 4 HOH A 6 306 135 HOH HOH . X 4 HOH A 7 307 21 HOH HOH . X 4 HOH A 8 308 141 HOH HOH . X 4 HOH A 9 309 138 HOH HOH . X 4 HOH A 10 310 47 HOH HOH . X 4 HOH A 11 311 149 HOH HOH . X 4 HOH A 12 312 48 HOH HOH . X 4 HOH A 13 313 41 HOH HOH . X 4 HOH A 14 314 50 HOH HOH . X 4 HOH A 15 315 152 HOH HOH . X 4 HOH A 16 316 22 HOH HOH . X 4 HOH A 17 317 4 HOH HOH . X 4 HOH A 18 318 197 HOH HOH . X 4 HOH A 19 319 198 HOH HOH . X 4 HOH A 20 320 5 HOH HOH . X 4 HOH A 21 321 143 HOH HOH . X 4 HOH A 22 322 139 HOH HOH . X 4 HOH A 23 323 150 HOH HOH . X 4 HOH A 24 324 65 HOH HOH . X 4 HOH A 25 325 88 HOH HOH . Y 4 HOH B 1 301 212 HOH HOH . Y 4 HOH B 2 302 70 HOH HOH . Y 4 HOH B 3 303 85 HOH HOH . Y 4 HOH B 4 304 86 HOH HOH . Y 4 HOH B 5 305 8 HOH HOH . Y 4 HOH B 6 306 134 HOH HOH . Y 4 HOH B 7 307 133 HOH HOH . Y 4 HOH B 8 308 87 HOH HOH . Y 4 HOH B 9 309 72 HOH HOH . Y 4 HOH B 10 310 40 HOH HOH . Y 4 HOH B 11 311 69 HOH HOH . Y 4 HOH B 12 312 129 HOH HOH . Y 4 HOH B 13 313 71 HOH HOH . Y 4 HOH B 14 314 131 HOH HOH . Y 4 HOH B 15 315 132 HOH HOH . Z 4 HOH C 1 301 125 HOH HOH . Z 4 HOH C 2 302 163 HOH HOH . Z 4 HOH C 3 303 107 HOH HOH . Z 4 HOH C 4 304 176 HOH HOH . Z 4 HOH C 5 305 121 HOH HOH . Z 4 HOH C 6 306 80 HOH HOH . Z 4 HOH C 7 307 14 HOH HOH . Z 4 HOH C 8 308 190 HOH HOH . AA 4 HOH D 1 301 106 HOH HOH . AA 4 HOH D 2 302 216 HOH HOH . AA 4 HOH D 3 303 164 HOH HOH . AA 4 HOH D 4 304 31 HOH HOH . AA 4 HOH D 5 305 170 HOH HOH . AA 4 HOH D 6 306 166 HOH HOH . AA 4 HOH D 7 307 19 HOH HOH . AA 4 HOH D 8 308 101 HOH HOH . AA 4 HOH D 9 309 34 HOH HOH . AA 4 HOH D 10 310 168 HOH HOH . AA 4 HOH D 11 311 240 HOH HOH . AA 4 HOH D 12 312 26 HOH HOH . AA 4 HOH D 13 313 108 HOH HOH . AA 4 HOH D 14 314 102 HOH HOH . AA 4 HOH D 15 315 115 HOH HOH . AA 4 HOH D 16 316 119 HOH HOH . AA 4 HOH D 17 317 219 HOH HOH . AA 4 HOH D 18 318 7 HOH HOH . AA 4 HOH D 19 319 112 HOH HOH . AA 4 HOH D 20 320 30 HOH HOH . AA 4 HOH D 21 321 98 HOH HOH . AA 4 HOH D 22 322 99 HOH HOH . AA 4 HOH D 23 323 111 HOH HOH . AA 4 HOH D 24 324 169 HOH HOH . AA 4 HOH D 25 325 105 HOH HOH . AA 4 HOH D 26 326 103 HOH HOH . AA 4 HOH D 27 327 114 HOH HOH . AA 4 HOH D 28 328 93 HOH HOH . AA 4 HOH D 29 329 116 HOH HOH . AA 4 HOH D 30 330 113 HOH HOH . BA 4 HOH H 1 301 64 HOH HOH . BA 4 HOH H 2 302 95 HOH HOH . BA 4 HOH H 3 303 33 HOH HOH . BA 4 HOH H 4 304 9 HOH HOH . BA 4 HOH H 5 305 167 HOH HOH . BA 4 HOH H 6 306 165 HOH HOH . BA 4 HOH H 7 307 76 HOH HOH . BA 4 HOH H 8 308 218 HOH HOH . BA 4 HOH H 9 309 63 HOH HOH . CA 4 HOH E 1 301 231 HOH HOH . CA 4 HOH E 2 302 29 HOH HOH . CA 4 HOH E 3 303 2 HOH HOH . CA 4 HOH E 4 304 128 HOH HOH . CA 4 HOH E 5 305 32 HOH HOH . CA 4 HOH E 6 306 28 HOH HOH . CA 4 HOH E 7 307 18 HOH HOH . CA 4 HOH E 8 308 78 HOH HOH . CA 4 HOH E 9 309 17 HOH HOH . CA 4 HOH E 10 310 13 HOH HOH . CA 4 HOH E 11 311 241 HOH HOH . CA 4 HOH E 12 312 130 HOH HOH . CA 4 HOH E 13 313 97 HOH HOH . CA 4 HOH E 14 314 79 HOH HOH . CA 4 HOH E 15 315 75 HOH HOH . DA 4 HOH F 1 301 147 HOH HOH . DA 4 HOH F 2 302 55 HOH HOH . DA 4 HOH F 3 303 10 HOH HOH . DA 4 HOH F 4 304 144 HOH HOH . DA 4 HOH F 5 305 137 HOH HOH . DA 4 HOH F 6 306 145 HOH HOH . DA 4 HOH F 7 307 12 HOH HOH . DA 4 HOH F 8 308 43 HOH HOH . DA 4 HOH F 9 309 142 HOH HOH . DA 4 HOH F 10 310 6 HOH HOH . DA 4 HOH F 11 311 59 HOH HOH . DA 4 HOH F 12 312 39 HOH HOH . DA 4 HOH F 13 313 58 HOH HOH . DA 4 HOH F 14 314 53 HOH HOH . DA 4 HOH F 15 315 82 HOH HOH . DA 4 HOH F 16 316 60 HOH HOH . DA 4 HOH F 17 317 136 HOH HOH . DA 4 HOH F 18 318 54 HOH HOH . DA 4 HOH F 19 319 56 HOH HOH . DA 4 HOH F 20 320 51 HOH HOH . DA 4 HOH F 21 321 146 HOH HOH . DA 4 HOH F 22 322 67 HOH HOH . DA 4 HOH F 23 323 83 HOH HOH . DA 4 HOH F 24 324 84 HOH HOH . DA 4 HOH F 25 325 96 HOH HOH . DA 4 HOH F 26 326 57 HOH HOH . DA 4 HOH F 27 327 68 HOH HOH . DA 4 HOH F 28 328 66 HOH HOH . EA 4 HOH G 1 301 120 HOH HOH . EA 4 HOH G 2 302 92 HOH HOH . EA 4 HOH G 3 303 232 HOH HOH . EA 4 HOH G 4 304 126 HOH HOH . EA 4 HOH G 5 305 122 HOH HOH . EA 4 HOH G 6 306 24 HOH HOH . EA 4 HOH G 7 307 188 HOH HOH . EA 4 HOH G 8 308 77 HOH HOH . EA 4 HOH G 9 309 127 HOH HOH . EA 4 HOH G 10 310 189 HOH HOH . EA 4 HOH G 11 311 35 HOH HOH . EA 4 HOH G 12 312 20 HOH HOH . EA 4 HOH G 13 313 16 HOH HOH . EA 4 HOH G 14 314 61 HOH HOH . EA 4 HOH G 15 315 104 HOH HOH . EA 4 HOH G 16 316 62 HOH HOH . EA 4 HOH G 17 317 185 HOH HOH . EA 4 HOH G 18 318 73 HOH HOH . FA 4 HOH I 1 301 171 HOH HOH . FA 4 HOH I 2 302 230 HOH HOH . FA 4 HOH I 3 303 186 HOH HOH . FA 4 HOH I 4 304 227 HOH HOH . FA 4 HOH I 5 305 182 HOH HOH . FA 4 HOH I 6 306 175 HOH HOH . GA 4 HOH J 1 201 179 HOH HOH . GA 4 HOH J 2 202 25 HOH HOH . GA 4 HOH J 3 203 52 HOH HOH . GA 4 HOH J 4 204 156 HOH HOH . GA 4 HOH J 5 205 94 HOH HOH . GA 4 HOH J 6 206 91 HOH HOH . GA 4 HOH J 7 207 23 HOH HOH . GA 4 HOH J 8 208 37 HOH HOH . HA 4 HOH K 1 301 237 HOH HOH . HA 4 HOH K 2 302 160 HOH HOH . HA 4 HOH K 3 303 173 HOH HOH . HA 4 HOH K 4 304 172 HOH HOH . HA 4 HOH K 5 305 214 HOH HOH . HA 4 HOH K 6 306 238 HOH HOH . HA 4 HOH K 7 307 161 HOH HOH . HA 4 HOH K 8 308 42 HOH HOH . HA 4 HOH K 9 309 183 HOH HOH . HA 4 HOH K 10 310 225 HOH HOH . IA 4 HOH L 1 301 208 HOH HOH . IA 4 HOH L 2 302 202 HOH HOH . IA 4 HOH L 3 303 204 HOH HOH . IA 4 HOH L 4 304 205 HOH HOH . IA 4 HOH L 5 305 157 HOH HOH . IA 4 HOH L 6 306 74 HOH HOH . IA 4 HOH L 7 307 203 HOH HOH . IA 4 HOH L 8 308 201 HOH HOH . IA 4 HOH L 9 309 27 HOH HOH . IA 4 HOH L 10 310 15 HOH HOH . IA 4 HOH L 11 311 3 HOH HOH . IA 4 HOH L 12 312 36 HOH HOH . IA 4 HOH L 13 313 38 HOH HOH . IA 4 HOH L 14 314 206 HOH HOH . IA 4 HOH L 15 315 89 HOH HOH . IA 4 HOH L 16 316 209 HOH HOH . IA 4 HOH L 17 317 90 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 C1 RET . . . S 3 -5.102 22.718 -47.454 1 50.41 ? C1 RET 201 F 1 HETATM 2 C C2 RET . . . S 3 -5.33 21.685 -48.552 1 38.17 ? C2 RET 201 F 1 HETATM 3 C C3 RET . . . S 3 -6.654 20.969 -48.428 1 47.09 ? C3 RET 201 F 1 HETATM 4 C C4 RET . . . S 3 -6.679 20.203 -47.127 1 57.82 ? C4 RET 201 F 1 HETATM 5 C C5 RET . . . S 3 -6.453 21.159 -45.986 1 64.01 ? C5 RET 201 F 1 HETATM 6 C C6 RET . . . S 3 -5.755 22.291 -46.13 1 57.78 ? C6 RET 201 F 1 HETATM 7 C C7 RET . . . S 3 -5.668 23.076 -44.877 1 60.56 ? C7 RET 201 F 1 HETATM 8 C C8 RET . . . S 3 -4.635 23.831 -44.538 1 58.02 ? C8 RET 201 F 1 HETATM 9 C C9 RET . . . S 3 -4.629 24.549 -43.271 1 60.45 ? C9 RET 201 F 1 HETATM 10 C C10 RET . . . S 3 -3.6 25.363 -43.05 1 58.03 ? C10 RET 201 F 1 HETATM 11 C C11 RET . . . S 3 -3.428 26.17 -41.849 1 58.7 ? C11 RET 201 F 1 HETATM 12 C C12 RET . . . S 3 -2.351 26.92 -41.981 1 59.68 ? C12 RET 201 F 1 HETATM 13 C C13 RET . . . S 3 -1.741 27.886 -41.05 1 54.57 ? C13 RET 201 F 1 HETATM 14 C C14 RET . . . S 3 -0.41 28.162 -41.191 1 61.42 ? C14 RET 201 F 1 HETATM 15 C C15 RET . . . S 3 0.32 29.116 -40.322 1 65.7 ? C15 RET 201 F 1 HETATM 16 C C16 RET . . . S 3 -5.645 24.08 -47.869 1 49.24 ? C16 RET 201 F 1 HETATM 17 C C17 RET . . . S 3 -3.58 22.812 -47.376 1 49.85 ? C17 RET 201 F 1 HETATM 18 C C18 RET . . . S 3 -7.048 20.826 -44.647 1 64.54 ? C18 RET 201 F 1 HETATM 19 C C19 RET . . . S 3 -5.758 24.392 -42.295 1 69.06 ? C19 RET 201 F 1 HETATM 20 C C20 RET . . . S 3 -2.716 28.403 -40.024 1 46.04 ? C20 RET 201 F 1 # _model_server_stats.io_time_ms 31 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #