data_8GRU # _model_server_result.job_id JaAfBdPlI6O8DF-oFkEigg _model_server_result.datetime_utc '2024-11-26 05:46:36' _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 8gru # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":401}' # _entry.id 8GRU # _exptl.entry_id 8GRU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 663.425 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description NICOTINAMIDE-ADENINE-DINUCLEOTIDE _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 8GRU _cell.length_a 134.043 _cell.length_b 163.833 _cell.length_c 163.129 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8GRU _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H 1 1 C,D,I,J,K,L 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 ? 3 E N N ? 3 H N N ? 3 I N N ? 3 L 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 C N GLY 264 C GLY 264 1_555 I O1A NAD . C NAD 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.315 ? metalc ? metalc1 A OD1 ASP 230 A ASP 230 1_555 F CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.568 ? metalc ? metalc2 F CA CA . A CA 402 1_555 G O7 ICT . A ICT 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.088 ? metalc ? metalc3 F CA CA . A CA 402 1_555 B OD2 ASP 217 B ASP 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.756 ? metalc ? metalc4 C OD1 ASP 230 C ASP 230 1_555 J CA CA . C CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? metalc ? metalc5 J CA CA . C CA 402 1_555 K O7 ICT . C ICT 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.756 ? metalc ? metalc6 J CA CA . C CA 402 1_555 D OD2 ASP 217 D ASP 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.838 ? # _chem_comp.formula 'C21 H27 N7 O14 P2' _chem_comp.formula_weight 663.425 _chem_comp.id NAD _chem_comp.mon_nstd_flag . _chem_comp.name NICOTINAMIDE-ADENINE-DINUCLEOTIDE _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 PA O1A NAD doub 255 n n PA O2A NAD sing 256 n n PA O5B NAD sing 257 n n PA O3 NAD sing 258 n n O2A HOA2 NAD sing 259 n n O5B C5B NAD sing 260 n n C5B C4B NAD sing 261 n n C5B H51A NAD sing 262 n n C5B H52A NAD sing 263 n n C4B O4B NAD sing 264 n n C4B C3B NAD sing 265 n n C4B H4B NAD sing 266 n n O4B C1B NAD sing 267 n n C3B O3B NAD sing 268 n n C3B C2B NAD sing 269 n n C3B H3B NAD sing 270 n n O3B HO3A NAD sing 271 n n C2B O2B NAD sing 272 n n C2B C1B NAD sing 273 n n C2B H2B NAD sing 274 n n O2B HO2A NAD sing 275 n n C1B N9A NAD sing 276 n n C1B H1B NAD sing 277 n n N9A C8A NAD sing 278 n y N9A C4A NAD sing 279 n y C8A N7A NAD doub 280 n y C8A H8A NAD sing 281 n n N7A C5A NAD sing 282 n y C5A C6A NAD sing 283 n y C5A C4A NAD doub 284 n y C6A N6A NAD sing 285 n n C6A N1A NAD doub 286 n y N6A H61A NAD sing 287 n n N6A H62A NAD sing 288 n n N1A C2A NAD sing 289 n y C2A N3A NAD doub 290 n y C2A H2A NAD sing 291 n n N3A C4A NAD sing 292 n y O3 PN NAD sing 293 n n PN O1N NAD doub 294 n n PN O2N NAD sing 295 n n PN O5D NAD sing 296 n n O5D C5D NAD sing 297 n n C5D C4D NAD sing 298 n n C5D H51N NAD sing 299 n n C5D H52N NAD sing 300 n n C4D O4D NAD sing 301 n n C4D C3D NAD sing 302 n n C4D H4D NAD sing 303 n n O4D C1D NAD sing 304 n n C3D O3D NAD sing 305 n n C3D C2D NAD sing 306 n n C3D H3D NAD sing 307 n n O3D HO3N NAD sing 308 n n C2D O2D NAD sing 309 n n C2D C1D NAD sing 310 n n C2D H2D NAD sing 311 n n O2D HO2N NAD sing 312 n n C1D N1N NAD sing 313 n n C1D H1D NAD sing 314 n n N1N C2N NAD sing 315 n y N1N C6N NAD doub 316 n y C2N C3N NAD doub 317 n y C2N H2N NAD sing 318 n n C3N C7N NAD sing 319 n n C3N C4N NAD sing 320 n y C7N O7N NAD doub 321 n n C7N N7N NAD sing 322 n n N7N H71N NAD sing 323 n n N7N H72N NAD sing 324 n n C4N C5N NAD doub 325 n y C4N H4N NAD sing 326 n n C5N C6N NAD sing 327 n y C5N H5N NAD sing 328 n n C6N H6N NAD sing 329 n n # _atom_sites.entry_id 8GRU _atom_sites.fract_transf_matrix[1][1] 0.00746 _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] 0.006104 _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] 0.00613 _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 3 NAD A 1 401 2 NAD NAD . F 4 CA A 1 402 1 CA CA . G 5 ICT A 1 403 2 ICT ICT . H 3 NAD B 1 401 1 NAD NAD . I 3 NAD C 1 401 4 NAD NAD . J 4 CA C 1 402 3 CA CA . K 5 ICT C 1 403 3 ICT ICT . L 3 NAD D 1 401 3 NAD NAD . # 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 NAD . . . I 3 -18.179 -0.998 -39.695 1 46.85 ? PA NAD 401 C 1 HETATM 2 O O1A NAD . . . I 3 -18.304 0.082 -38.523 1 69.4 ? O1A NAD 401 C 1 HETATM 3 O O2A NAD . . . I 3 -16.732 -1.371 -39.949 1 46.96 ? O2A NAD 401 C 1 HETATM 4 O O5B NAD . . . I 3 -18.858 -0.476 -41.148 1 54.93 ? O5B NAD 401 C 1 HETATM 5 C C5B NAD . . . I 3 -18.591 -1.352 -42.238 1 57.64 ? C5B NAD 401 C 1 HETATM 6 C C4B NAD . . . I 3 -18.284 -0.507 -43.554 1 55.34 ? C4B NAD 401 C 1 HETATM 7 O O4B NAD . . . I 3 -18.896 0.67 -43.444 1 54 ? O4B NAD 401 C 1 HETATM 8 C C3B NAD . . . I 3 -16.799 -0.149 -43.751 1 61.77 ? C3B NAD 401 C 1 HETATM 9 O O3B NAD . . . I 3 -16.116 -1.001 -44.566 1 68.68 ? O3B NAD 401 C 1 HETATM 10 C C2B NAD . . . I 3 -16.9 1.123 -44.621 1 60.59 ? C2B NAD 401 C 1 HETATM 11 O O2B NAD . . . I 3 -17.391 0.647 -45.938 1 75.96 ? O2B NAD 401 C 1 HETATM 12 C C1B NAD . . . I 3 -17.834 1.76 -44.036 1 59.1 ? C1B NAD 401 C 1 HETATM 13 N N9A NAD . . . I 3 -17.326 2.7 -43.012 1 58.69 ? N9A NAD 401 C 1 HETATM 14 C C8A NAD . . . I 3 -17.484 2.538 -41.7 1 60.06 ? C8A NAD 401 C 1 HETATM 15 N N7A NAD . . . I 3 -16.916 3.577 -41.074 1 54.23 ? N7A NAD 401 C 1 HETATM 16 C C5A NAD . . . I 3 -16.408 4.4 -42.013 1 53.16 ? C5A NAD 401 C 1 HETATM 17 C C6A NAD . . . I 3 -15.722 5.603 -41.947 1 58.2 ? C6A NAD 401 C 1 HETATM 18 N N6A NAD . . . I 3 -15.36 6.317 -40.731 1 57.89 ? N6A NAD 401 C 1 HETATM 19 N N1A NAD . . . I 3 -15.309 6.23 -43.051 1 52.87 ? N1A NAD 401 C 1 HETATM 20 C C2A NAD . . . I 3 -15.588 5.647 -44.254 1 55.62 ? C2A NAD 401 C 1 HETATM 21 N N3A NAD . . . I 3 -16.256 4.476 -44.336 1 58.54 ? N3A NAD 401 C 1 HETATM 22 C C4A NAD . . . I 3 -16.666 3.852 -43.227 1 56.61 ? C4A NAD 401 C 1 HETATM 23 O O3 NAD . . . I 3 -18.956 -2.452 -39.373 1 53.16 ? O3 NAD 401 C 1 HETATM 24 P PN NAD . . . I 3 -18.63 -3.994 -39.901 1 37.82 ? PN NAD 401 C 1 HETATM 25 O O1N NAD . . . I 3 -17.878 -4.007 -41.212 1 49.08 ? O1N NAD 401 C 1 HETATM 26 O O2N NAD . . . I 3 -19.919 -4.785 -39.918 1 37.09 ? O2N NAD 401 C 1 HETATM 27 O O5D NAD . . . I 3 -17.661 -4.779 -38.874 1 51.99 ? O5D NAD 401 C 1 HETATM 28 C C5D NAD . . . I 3 -17.133 -3.966 -37.922 1 47.69 ? C5D NAD 401 C 1 HETATM 29 C C4D NAD . . . I 3 -16.236 -4.713 -37.052 1 42.9 ? C4D NAD 401 C 1 HETATM 30 O O4D NAD . . . I 3 -15.91 -3.799 -36.173 1 53.76 ? O4D NAD 401 C 1 HETATM 31 C C3D NAD . . . I 3 -17.043 -5.852 -36.195 1 43.03 ? C3D NAD 401 C 1 HETATM 32 O O3D NAD . . . I 3 -15.989 -6.699 -35.623 1 49.78 ? O3D NAD 401 C 1 HETATM 33 C C2D NAD . . . I 3 -17.65 -5.207 -35.297 1 45.54 ? C2D NAD 401 C 1 HETATM 34 O O2D NAD . . . I 3 -17.837 -5.833 -33.949 1 46.82 ? O2D NAD 401 C 1 HETATM 35 C C1D NAD . . . I 3 -16.765 -3.92 -34.962 1 50.38 ? C1D NAD 401 C 1 HETATM 36 N N1N NAD . . . I 3 -17.522 -2.871 -34.696 1 57.66 ? N1N NAD 401 C 1 HETATM 37 C C2N NAD . . . I 3 -17.27 -2.123 -33.585 1 58.08 ? C2N NAD 401 C 1 HETATM 38 C C3N NAD . . . I 3 -18.127 -1.105 -33.191 1 53.45 ? C3N NAD 401 C 1 HETATM 39 C C7N NAD . . . I 3 -17.787 -0.266 -31.922 1 53.15 ? C7N NAD 401 C 1 HETATM 40 O O7N NAD . . . I 3 -18.372 0.733 -31.648 1 54.47 ? O7N NAD 401 C 1 HETATM 41 N N7N NAD . . . I 3 -16.705 -0.7 -31.034 1 61.42 ? N7N NAD 401 C 1 HETATM 42 C C4N NAD . . . I 3 -19.218 -0.776 -33.944 1 53.92 ? C4N NAD 401 C 1 HETATM 43 C C5N NAD . . . I 3 -19.48 -1.574 -35.021 1 53.19 ? C5N NAD 401 C 1 HETATM 44 C C6N NAD . . . I 3 -18.637 -2.607 -35.388 1 54.72 ? C6N NAD 401 C 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 262 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 44 #