data_5CEE # _model_server_result.job_id weB9-HfPrHhF9plQy36Tog _model_server_result.datetime_utc '2024-11-29 14:00:22' _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 5cee # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5CEE # _exptl.entry_id 5CEE _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 663.425 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description NICOTINAMIDE-ADENINE-DINUCLEOTIDE _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 5CEE _cell.length_a 48.236 _cell.length_b 48.236 _cell.length_c 291.068 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5CEE _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 5_554 x-y,-y,-z-1/3 1 0 0 0 -1 0 0 0 -1 0 0 -97.022667 # _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 metalc ? metalc1 A OE2 GLU 156 A GLU 133 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc2 A OD1 ASP 157 A ASP 134 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.926 ? metalc ? metalc3 A OD1 ASP 182 A ASP 159 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.22 ? metalc ? metalc4 A OD2 ASP 182 A ASP 159 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.785 ? metalc ? metalc5 C MG MG . A MG 402 1_555 D O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc6 C MG MG . A MG 402 1_555 D O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.123 ? metalc ? metalc7 C MG MG . A MG 402 1_555 D O HOH . A HOH 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? # _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 237 n n PA O2A NAD sing 238 n n PA O5B NAD sing 239 n n PA O3 NAD sing 240 n n O2A HOA2 NAD sing 241 n n O5B C5B NAD sing 242 n n C5B C4B NAD sing 243 n n C5B H51A NAD sing 244 n n C5B H52A NAD sing 245 n n C4B O4B NAD sing 246 n n C4B C3B NAD sing 247 n n C4B H4B NAD sing 248 n n O4B C1B NAD sing 249 n n C3B O3B NAD sing 250 n n C3B C2B NAD sing 251 n n C3B H3B NAD sing 252 n n O3B HO3A NAD sing 253 n n C2B O2B NAD sing 254 n n C2B C1B NAD sing 255 n n C2B H2B NAD sing 256 n n O2B HO2A NAD sing 257 n n C1B N9A NAD sing 258 n n C1B H1B NAD sing 259 n n N9A C8A NAD sing 260 n y N9A C4A NAD sing 261 n y C8A N7A NAD doub 262 n y C8A H8A NAD sing 263 n n N7A C5A NAD sing 264 n y C5A C6A NAD sing 265 n y C5A C4A NAD doub 266 n y C6A N6A NAD sing 267 n n C6A N1A NAD doub 268 n y N6A H61A NAD sing 269 n n N6A H62A NAD sing 270 n n N1A C2A NAD sing 271 n y C2A N3A NAD doub 272 n y C2A H2A NAD sing 273 n n N3A C4A NAD sing 274 n y O3 PN NAD sing 275 n n PN O1N NAD doub 276 n n PN O2N NAD sing 277 n n PN O5D NAD sing 278 n n O5D C5D NAD sing 279 n n C5D C4D NAD sing 280 n n C5D H51N NAD sing 281 n n C5D H52N NAD sing 282 n n C4D O4D NAD sing 283 n n C4D C3D NAD sing 284 n n C4D H4D NAD sing 285 n n O4D C1D NAD sing 286 n n C3D O3D NAD sing 287 n n C3D C2D NAD sing 288 n n C3D H3D NAD sing 289 n n O3D HO3N NAD sing 290 n n C2D O2D NAD sing 291 n n C2D C1D NAD sing 292 n n C2D H2D NAD sing 293 n n O2D HO2N NAD sing 294 n n C1D N1N NAD sing 295 n n C1D H1D NAD sing 296 n n N1N C2N NAD sing 297 n y N1N C6N NAD doub 298 n y C2N C3N NAD doub 299 n y C2N H2N NAD sing 300 n n C3N C7N NAD sing 301 n n C3N C4N NAD sing 302 n y C7N O7N NAD doub 303 n n C7N N7N NAD sing 304 n n N7N H71N NAD sing 305 n n N7N H72N NAD sing 306 n n C4N C5N NAD doub 307 n y C4N H4N NAD sing 308 n n C5N C6N NAD sing 309 n y C5N H5N NAD sing 310 n n C6N H6N NAD sing 311 n n # _atom_sites.entry_id 5CEE _atom_sites.fract_transf_matrix[1][1] 0.020731 _atom_sites.fract_transf_matrix[1][2] 0.011969 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.023939 _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] 0.003436 _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 NAD A 1 401 1 NAD NAD . C 3 MG A 1 402 1 MG MG . D 4 HOH A 1 501 11 HOH HOH . D 4 HOH A 2 502 5 HOH HOH . D 4 HOH A 3 503 12 HOH HOH . D 4 HOH A 4 504 3 HOH HOH . D 4 HOH A 5 505 8 HOH HOH . D 4 HOH A 6 506 1 HOH HOH . D 4 HOH A 7 507 13 HOH HOH . D 4 HOH A 8 508 2 HOH HOH . D 4 HOH A 9 509 4 HOH HOH . D 4 HOH A 10 510 9 HOH HOH . D 4 HOH A 11 511 6 HOH HOH . D 4 HOH A 12 512 10 HOH HOH . D 4 HOH A 13 513 7 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 NAD . . . B 2 9.739 13.594 -26.679 1 45.36 ? PA NAD 401 A 1 HETATM 2 O O1A NAD . . . B 2 9.196 14.82 -27.363 1 47.07 1 O1A NAD 401 A 1 HETATM 3 O O2A NAD . . . B 2 9.177 12.232 -27.011 1 40 ? O2A NAD 401 A 1 HETATM 4 O O5B NAD . . . B 2 9.57 13.805 -25.095 1 43.47 ? O5B NAD 401 A 1 HETATM 5 C C5B NAD . . . B 2 9.126 15.07 -24.636 1 42.93 ? C5B NAD 401 A 1 HETATM 6 C C4B NAD . . . B 2 7.883 14.891 -23.79 1 43.2 ? C4B NAD 401 A 1 HETATM 7 O O4B NAD . . . B 2 8.058 15.688 -22.623 1 48.3 ? O4B NAD 401 A 1 HETATM 8 C C3B NAD . . . B 2 6.647 15.412 -24.504 1 43.38 ? C3B NAD 401 A 1 HETATM 9 O O3B NAD . . . B 2 5.782 14.341 -24.888 1 46.66 ? O3B NAD 401 A 1 HETATM 10 C C2B NAD . . . B 2 5.939 16.309 -23.513 1 46.56 ? C2B NAD 401 A 1 HETATM 11 O O2B NAD . . . B 2 4.746 15.648 -23.102 1 47.53 ? O2B NAD 401 A 1 HETATM 12 C C1B NAD . . . B 2 6.866 16.41 -22.317 1 45.39 ? C1B NAD 401 A 1 HETATM 13 N N9A NAD . . . B 2 7.252 17.806 -21.996 1 45.35 ? N9A NAD 401 A 1 HETATM 14 C C8A NAD . . . B 2 7.664 18.746 -22.866 1 44.78 ? C8A NAD 401 A 1 HETATM 15 N N7A NAD . . . B 2 7.949 19.91 -22.229 1 46.61 ? N7A NAD 401 A 1 HETATM 16 C C5A NAD . . . B 2 7.717 19.715 -20.915 1 49.58 ? C5A NAD 401 A 1 HETATM 17 C C6A NAD . . . B 2 7.814 20.525 -19.677 1 49.19 ? C6A NAD 401 A 1 HETATM 18 N N6A NAD . . . B 2 8.225 21.819 -19.717 1 49.33 ? N6A NAD 401 A 1 HETATM 19 N N1A NAD . . . B 2 7.478 19.928 -18.509 1 50.82 ? N1A NAD 401 A 1 HETATM 20 C C2A NAD . . . B 2 7.069 18.645 -18.452 1 45.32 ? C2A NAD 401 A 1 HETATM 21 N N3A NAD . . . B 2 6.957 17.852 -19.529 1 45.39 ? N3A NAD 401 A 1 HETATM 22 C C4A NAD . . . B 2 7.257 18.326 -20.767 1 47.5 ? C4A NAD 401 A 1 HETATM 23 O O3 NAD . . . B 2 11.336 13.643 -26.898 1 38.26 ? O3 NAD 401 A 1 HETATM 24 P PN NAD . . . B 2 12.335 12.564 -26.252 1 43.52 ? PN NAD 401 A 1 HETATM 25 O O1N NAD . . . B 2 12.924 11.692 -27.332 1 41.07 1 O1N NAD 401 A 1 HETATM 26 O O2N NAD . . . B 2 11.616 11.913 -25.093 1 39.7 ? O2N NAD 401 A 1 HETATM 27 O O5D NAD . . . B 2 13.493 13.552 -25.725 1 36.69 ? O5D NAD 401 A 1 HETATM 28 C C5D NAD . . . B 2 13.24 14.324 -24.555 1 37.78 ? C5D NAD 401 A 1 HETATM 29 C C4D NAD . . . B 2 14.466 15.145 -24.195 1 39.89 ? C4D NAD 401 A 1 HETATM 30 O O4D NAD . . . B 2 15.422 14.295 -23.556 1 38.75 ? O4D NAD 401 A 1 HETATM 31 C C3D NAD . . . B 2 15.092 15.73 -25.448 1 35.63 ? C3D NAD 401 A 1 HETATM 32 O O3D NAD . . . B 2 15.287 17.135 -25.255 1 32.34 ? O3D NAD 401 A 1 HETATM 33 C C2D NAD . . . B 2 16.407 14.983 -25.624 1 38.9 ? C2D NAD 401 A 1 HETATM 34 O O2D NAD . . . B 2 17.515 15.834 -25.938 1 39.36 ? O2D NAD 401 A 1 HETATM 35 C C1D NAD . . . B 2 16.648 14.303 -24.288 1 36.92 ? C1D NAD 401 A 1 HETATM 36 N N1N NAD . . . B 2 17.187 12.959 -24.498 1 35.61 ? N1N NAD 401 A 1 HETATM 37 C C2N NAD . . . B 2 18.458 12.78 -24.176 1 38.55 ? C2N NAD 401 A 1 HETATM 38 C C3N NAD . . . B 2 19.074 11.556 -24.339 1 40.44 ? C3N NAD 401 A 1 HETATM 39 C C7N NAD . . . B 2 20.514 11.466 -23.932 1 35.4 ? C7N NAD 401 A 1 HETATM 40 O O7N NAD . . . B 2 21.045 12.47 -23.49 1 30.76 ? O7N NAD 401 A 1 HETATM 41 N N7N NAD . . . B 2 21.156 10.31 -24.066 1 36.59 ? N7N NAD 401 A 1 HETATM 42 C C4N NAD . . . B 2 18.35 10.48 -24.849 1 35.73 ? C4N NAD 401 A 1 HETATM 43 C C5N NAD . . . B 2 17.015 10.683 -25.182 1 34.51 ? C5N NAD 401 A 1 HETATM 44 C C6N NAD . . . B 2 16.454 11.95 -24.998 1 40.69 ? C6N NAD 401 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 44 #