data_3RNO # _model_server_result.job_id RiU502tkxaXJ6CajKeO76A _model_server_result.datetime_utc '2024-11-22 09:15:26' _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 3rno # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":265}' # _entry.id 3RNO # _exptl.entry_id 3RNO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 743.405 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _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 3RNO _cell.length_a 126.664 _cell.length_b 126.664 _cell.length_c 108.494 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RNO _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # 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 author_and_software_defined_assembly 2 PISA hexameric 6 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C 1 1,2 A,B,C 2 1,3 A,B,C 3 1,4,5,3,6,7 # 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' 17_555 x-y+1/3,-y+2/3,-z+2/3 1 0 0 0 -1 0 0 0 -1 0 73.129494 72.329333 3 'crystal symmetry operation' 4_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 108.494 4 'crystal symmetry operation' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 5 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 6 'crystal symmetry operation' 5_556 x-y,-y,-z+1 1 0 0 0 -1 0 0 0 -1 0 0 108.494 7 'crystal symmetry operation' 6_556 -x,-x+y,-z+1 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 108.494 # _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 # 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 C LEU 54 A LEU 53 1_555 A N MSE 55 A MSE 54 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.301 ? covale ? covale2 A C MSE 55 A MSE 54 1_555 A N GLU 56 A GLU 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale3 A C SER 74 A SER 73 1_555 A N MSE 75 A MSE 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale4 A C MSE 75 A MSE 74 1_555 A N SER 76 A SER 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.315 ? covale ? covale5 A C LYS 131 A LYS 130 1_555 A N MSE 132 A MSE 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale6 A C MSE 132 A MSE 131 1_555 A N ASP 133 A ASP 132 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale7 A C GLU 139 A GLU 138 1_555 A N MSE 140 A MSE 139 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale8 A C MSE 140 A MSE 139 1_555 A N PRO 141 A PRO 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.36 ? covale ? covale9 A C PRO 144 A PRO 143 1_555 A N MSE 145 A MSE 144 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.303 ? covale ? covale10 A C MSE 145 A MSE 144 1_555 A N MSE 146 A MSE 145 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.316 ? covale ? covale11 A C MSE 146 A MSE 145 1_555 A N VAL 147 A VAL 146 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? # _chem_comp.formula 'C21 H28 N7 O17 P3' _chem_comp.formula_weight 743.405 _chem_comp.id NAP _chem_comp.mon_nstd_flag . _chem_comp.name 'NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE" # 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 PA O1A NAP doub 237 n n PA O2A NAP sing 238 n n PA O5B NAP sing 239 n n PA O3 NAP sing 240 n n O2A HOA2 NAP sing 241 n n O5B C5B NAP sing 242 n n C5B C4B NAP sing 243 n n C5B H51A NAP sing 244 n n C5B H52A NAP sing 245 n n C4B O4B NAP sing 246 n n C4B C3B NAP sing 247 n n C4B H4B NAP sing 248 n n O4B C1B NAP sing 249 n n C3B O3B NAP sing 250 n n C3B C2B NAP sing 251 n n C3B H3B NAP sing 252 n n O3B HO3A NAP sing 253 n n C2B O2B NAP sing 254 n n C2B C1B NAP sing 255 n n C2B H2B NAP sing 256 n n O2B P2B NAP sing 257 n n C1B N9A NAP sing 258 n n C1B H1B NAP sing 259 n n N9A C8A NAP sing 260 n y N9A C4A NAP sing 261 n y C8A N7A NAP doub 262 n y C8A H8A NAP sing 263 n n N7A C5A NAP sing 264 n y C5A C6A NAP sing 265 n y C5A C4A NAP doub 266 n y C6A N6A NAP sing 267 n n C6A N1A NAP doub 268 n y N6A H61A NAP sing 269 n n N6A H62A NAP sing 270 n n N1A C2A NAP sing 271 n y C2A N3A NAP doub 272 n y C2A H2A NAP sing 273 n n N3A C4A NAP sing 274 n y O3 PN NAP sing 275 n n PN O1N NAP doub 276 n n PN O2N NAP sing 277 n n PN O5D NAP sing 278 n n O5D C5D NAP sing 279 n n C5D C4D NAP sing 280 n n C5D H51N NAP sing 281 n n C5D H52N NAP sing 282 n n C4D O4D NAP sing 283 n n C4D C3D NAP sing 284 n n C4D H4D NAP sing 285 n n O4D C1D NAP sing 286 n n C3D O3D NAP sing 287 n n C3D C2D NAP sing 288 n n C3D H3D NAP sing 289 n n O3D HO3N NAP sing 290 n n C2D O2D NAP sing 291 n n C2D C1D NAP sing 292 n n C2D H2D NAP sing 293 n n O2D HO2N NAP sing 294 n n C1D N1N NAP sing 295 n n C1D H1D NAP sing 296 n n N1N C2N NAP sing 297 n y N1N C6N NAP doub 298 n y C2N C3N NAP doub 299 n y C2N H2N NAP sing 300 n n C3N C7N NAP sing 301 n n C3N C4N NAP sing 302 n y C7N O7N NAP doub 303 n n C7N N7N NAP sing 304 n n N7N H71N NAP sing 305 n n N7N H72N NAP sing 306 n n C4N C5N NAP doub 307 n y C4N H4N NAP sing 308 n n C5N C6N NAP sing 309 n y C5N H5N NAP sing 310 n n C6N H6N NAP sing 311 n n P2B O1X NAP doub 312 n n P2B O2X NAP sing 313 n n P2B O3X NAP sing 314 n n O2X HOP2 NAP sing 315 n n O3X HOP3 NAP sing 316 n n # _atom_sites.entry_id 3RNO _atom_sites.fract_transf_matrix[1][1] 0.007895 _atom_sites.fract_transf_matrix[1][2] 0.004558 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009116 _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] 0.009217 _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 NAP A 1 265 1 NAP NAP . C 3 HOH A 1 266 1 HOH HOH . C 3 HOH A 2 267 2 HOH HOH . C 3 HOH A 3 268 3 HOH HOH . C 3 HOH A 4 269 4 HOH HOH . C 3 HOH A 5 270 5 HOH HOH . C 3 HOH A 6 271 6 HOH HOH . C 3 HOH A 7 272 7 HOH HOH . C 3 HOH A 8 273 8 HOH HOH . C 3 HOH A 9 274 9 HOH HOH . C 3 HOH A 10 275 10 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 P PA NAP . . . B 2 16.273 18.831 30.885 1 110.01 ? PA NAP 265 A 1 HETATM 2 O O1A NAP . . . B 2 15.073 18.235 30.259 1 109.21 ? O1A NAP 265 A 1 HETATM 3 O O2A NAP . . . B 2 16.026 19.551 32.147 1 108.18 ? O2A NAP 265 A 1 HETATM 4 O O5B NAP . . . B 2 17.37 17.662 31.097 1 113.59 ? O5B NAP 265 A 1 HETATM 5 C C5B NAP . . . B 2 18.616 17.578 30.416 1 117.11 ? C5B NAP 265 A 1 HETATM 6 C C4B NAP . . . B 2 19.72 17.151 31.383 1 118.92 ? C4B NAP 265 A 1 HETATM 7 O O4B NAP . . . B 2 19.177 16.09 32.14 1 120.57 ? O4B NAP 265 A 1 HETATM 8 C C3B NAP . . . B 2 21.02 16.59 30.781 1 120.41 ? C3B NAP 265 A 1 HETATM 9 O O3B NAP . . . B 2 22.037 17.541 30.55 1 119.14 ? O3B NAP 265 A 1 HETATM 10 C C2B NAP . . . B 2 21.424 15.545 31.815 1 121.85 ? C2B NAP 265 A 1 HETATM 11 O O2B NAP . . . B 2 22.037 16.11 32.984 1 123.41 ? O2B NAP 265 A 1 HETATM 12 C C1B NAP . . . B 2 20.064 14.974 32.208 1 121.64 ? C1B NAP 265 A 1 HETATM 13 N N9A NAP . . . B 2 19.567 13.808 31.395 1 121.67 ? N9A NAP 265 A 1 HETATM 14 C C8A NAP . . . B 2 19.089 13.801 30.091 1 120.97 ? C8A NAP 265 A 1 HETATM 15 N N7A NAP . . . B 2 18.714 12.53 29.787 1 120.74 ? N7A NAP 265 A 1 HETATM 16 C C5A NAP . . . B 2 18.935 11.713 30.861 1 120.75 ? C5A NAP 265 A 1 HETATM 17 C C6A NAP . . . B 2 18.742 10.336 31.098 1 120.47 ? C6A NAP 265 A 1 HETATM 18 N N6A NAP . . . B 2 18.242 9.55 30.144 1 120.11 ? N6A NAP 265 A 1 HETATM 19 N N1A NAP . . . B 2 19.074 9.781 32.334 1 119.88 ? N1A NAP 265 A 1 HETATM 20 C C2A NAP . . . B 2 19.59 10.578 33.347 1 119.35 ? C2A NAP 265 A 1 HETATM 21 N N3A NAP . . . B 2 19.782 11.934 33.111 1 119.49 ? N3A NAP 265 A 1 HETATM 22 C C4A NAP . . . B 2 19.466 12.503 31.89 1 120.99 ? C4A NAP 265 A 1 HETATM 23 O O3 NAP . . . B 2 16.858 19.845 29.775 1 112.71 ? O3 NAP 265 A 1 HETATM 24 P PN NAP . . . B 2 17.579 21.305 29.787 1 112.36 ? PN NAP 265 A 1 HETATM 25 O O1N NAP . . . B 2 18.077 21.551 31.167 1 112.25 ? O1N NAP 265 A 1 HETATM 26 O O2N NAP . . . B 2 18.556 21.349 28.68 1 112.11 ? O2N NAP 265 A 1 HETATM 27 O O5D NAP . . . B 2 16.386 22.329 29.371 1 112.35 ? O5D NAP 265 A 1 HETATM 28 C C5D NAP . . . B 2 15.18 21.979 28.706 1 113.34 ? C5D NAP 265 A 1 HETATM 29 C C4D NAP . . . B 2 13.941 22.36 29.55 1 114.46 ? C4D NAP 265 A 1 HETATM 30 O O4D NAP . . . B 2 14.006 23.668 30.136 1 114.79 ? O4D NAP 265 A 1 HETATM 31 C C3D NAP . . . B 2 12.653 22.354 28.724 1 114.53 ? C3D NAP 265 A 1 HETATM 32 O O3D NAP . . . B 2 11.767 21.354 29.165 1 113.41 ? O3D NAP 265 A 1 HETATM 33 C C2D NAP . . . B 2 12.079 23.758 28.891 1 114.64 ? C2D NAP 265 A 1 HETATM 34 O O2D NAP . . . B 2 10.676 23.775 28.989 1 115.99 ? O2D NAP 265 A 1 HETATM 35 C C1D NAP . . . B 2 12.717 24.25 30.175 1 113.92 ? C1D NAP 265 A 1 HETATM 36 N N1N NAP . . . B 2 12.729 25.725 30.257 1 112.91 ? N1N NAP 265 A 1 HETATM 37 P P2B NAP . . . B 2 22.959 15.317 34.093 1 125.07 ? P2B NAP 265 A 1 HETATM 38 O O1X NAP . . . B 2 22.198 14.151 34.713 1 124.95 ? O1X NAP 265 A 1 HETATM 39 O O2X NAP . . . B 2 23.392 16.197 35.262 1 123.39 ? O2X NAP 265 A 1 HETATM 40 O O3X NAP . . . B 2 24.173 14.806 33.331 1 124.84 ? O3X NAP 265 A 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 401 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 40 #