data_1GPD # _model_server_result.job_id sTjYzzbKsZr6-HQYNS-R_A _model_server_result.datetime_utc '2024-12-26 09:51:11' _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 1gpd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":335}' # _entry.id 1GPD # _exptl.entry_id 1GPD _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 2 _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 1GPD _cell.length_a 149 _cell.length_b 139.1 _cell.length_c 80.7 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1GPD _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _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 'point symmetry operation' ? ? -0.170476 -0.748321 -0.640255 -0.74878 -0.324519 0.577934 -0.641323 0.578543 -0.505006 96.24453 70.94252 41.77925 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 H 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 C ACE 1 G ACE 0 1_555 A N SER 2 G SER 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? covale ? covale2 B C ACE 1 R ACE 0 1_555 B N SER 2 R SER 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? # _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 241 n n PA O2A NAD sing 242 n n PA O5B NAD sing 243 n n PA O3 NAD sing 244 n n O2A HOA2 NAD sing 245 n n O5B C5B NAD sing 246 n n C5B C4B NAD sing 247 n n C5B H51A NAD sing 248 n n C5B H52A NAD sing 249 n n C4B O4B NAD sing 250 n n C4B C3B NAD sing 251 n n C4B H4B NAD sing 252 n n O4B C1B NAD sing 253 n n C3B O3B NAD sing 254 n n C3B C2B NAD sing 255 n n C3B H3B NAD sing 256 n n O3B HO3A NAD sing 257 n n C2B O2B NAD sing 258 n n C2B C1B NAD sing 259 n n C2B H2B NAD sing 260 n n O2B HO2A NAD sing 261 n n C1B N9A NAD sing 262 n n C1B H1B NAD sing 263 n n N9A C8A NAD sing 264 n y N9A C4A NAD sing 265 n y C8A N7A NAD doub 266 n y C8A H8A NAD sing 267 n n N7A C5A NAD sing 268 n y C5A C6A NAD sing 269 n y C5A C4A NAD doub 270 n y C6A N6A NAD sing 271 n n C6A N1A NAD doub 272 n y N6A H61A NAD sing 273 n n N6A H62A NAD sing 274 n n N1A C2A NAD sing 275 n y C2A N3A NAD doub 276 n y C2A H2A NAD sing 277 n n N3A C4A NAD sing 278 n y O3 PN NAD sing 279 n n PN O1N NAD doub 280 n n PN O2N NAD sing 281 n n PN O5D NAD sing 282 n n O5D C5D NAD sing 283 n n C5D C4D NAD sing 284 n n C5D H51N NAD sing 285 n n C5D H52N NAD sing 286 n n C4D O4D NAD sing 287 n n C4D C3D NAD sing 288 n n C4D H4D NAD sing 289 n n O4D C1D NAD sing 290 n n C3D O3D NAD sing 291 n n C3D C2D NAD sing 292 n n C3D H3D NAD sing 293 n n O3D HO3N NAD sing 294 n n C2D O2D NAD sing 295 n n C2D C1D NAD sing 296 n n C2D H2D NAD sing 297 n n O2D HO2N NAD sing 298 n n C1D N1N NAD sing 299 n n C1D H1D NAD sing 300 n n N1N C2N NAD sing 301 n y N1N C6N NAD doub 302 n y C2N C3N NAD doub 303 n y C2N H2N NAD sing 304 n n C3N C7N NAD sing 305 n n C3N C4N NAD sing 306 n y C7N O7N NAD doub 307 n n C7N N7N NAD sing 308 n n N7N H71N NAD sing 309 n n N7N H72N NAD sing 310 n n C4N C5N NAD doub 311 n y C4N H4N NAD sing 312 n n C5N C6N NAD sing 313 n y C5N H5N NAD sing 314 n n C6N H6N NAD sing 315 n n # _atom_sites.entry_id 1GPD _atom_sites.fract_transf_matrix[1][1] 0.006711 _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] 0.007189 _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] 0.012392 _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 C 2 NAD G 1 335 1 NAD NAD . D 3 PO4 R 1 335 2 PO4 SPS . E 3 PO4 R 1 336 3 PO4 IPS . F 3 PO4 R 1 337 2 PO4 SPS . G 3 PO4 R 1 338 3 PO4 IPS . H 2 NAD R 1 339 1 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 . . . C 2 67.461 34.682 -7.697 1 0 ? PA NAD 335 G 1 HETATM 2 O O1A NAD . . . C 2 66.379 33.804 -8.194 1 0 ? O1A NAD 335 G 1 HETATM 3 O O2A NAD . . . C 2 67.331 34.961 -6.248 1 0 ? O2A NAD 335 G 1 HETATM 4 O O5B NAD . . . C 2 67.466 35.893 -8.745 1 0 ? O5B NAD 335 G 1 HETATM 5 C C5B NAD . . . C 2 66.296 36.126 -9.55 1 0 ? C5B NAD 335 G 1 HETATM 6 C C4B NAD . . . C 2 65.783 37.534 -9.323 1 0 ? C4B NAD 335 G 1 HETATM 7 O O4B NAD . . . C 2 66.618 38.467 -10.067 1 0 ? O4B NAD 335 G 1 HETATM 8 C C3B NAD . . . C 2 64.371 37.818 -9.835 1 0 ? C3B NAD 335 G 1 HETATM 9 O O3B NAD . . . C 2 63.378 37.403 -8.907 1 0 ? O3B NAD 335 G 1 HETATM 10 C C2B NAD . . . C 2 64.405 39.331 -10.049 1 0 ? C2B NAD 335 G 1 HETATM 11 O O2B NAD . . . C 2 64.31 40.015 -8.811 1 0 ? O2B NAD 335 G 1 HETATM 12 C C1B NAD . . . C 2 65.826 39.536 -10.561 1 0 ? C1B NAD 335 G 1 HETATM 13 N N9A NAD . . . C 2 65.933 39.536 -12.048 1 0 ? N9A NAD 335 G 1 HETATM 14 C C8A NAD . . . C 2 66.888 40.124 -12.849 1 0 ? C8A NAD 335 G 1 HETATM 15 N N7A NAD . . . C 2 66.697 39.941 -14.119 1 0 ? N7A NAD 335 G 1 HETATM 16 C C5A NAD . . . C 2 65.537 39.181 -14.177 1 0 ? C5A NAD 335 G 1 HETATM 17 C C6A NAD . . . C 2 64.803 38.652 -15.251 1 0 ? C6A NAD 335 G 1 HETATM 18 N N6A NAD . . . C 2 65.149 38.819 -16.537 1 0 ? N6A NAD 335 G 1 HETATM 19 N N1A NAD . . . C 2 63.698 37.944 -14.958 1 0 ? N1A NAD 335 G 1 HETATM 20 C C2A NAD . . . C 2 63.361 37.782 -13.678 1 0 ? C2A NAD 335 G 1 HETATM 21 N N3A NAD . . . C 2 63.963 38.225 -12.596 1 0 ? N3A NAD 335 G 1 HETATM 22 C C4A NAD . . . C 2 65.066 38.931 -12.919 1 0 ? C4A NAD 335 G 1 HETATM 23 O O3 NAD . . . C 2 68.88 34.005 -7.989 1 0 ? O3 NAD 335 G 1 HETATM 24 P PN NAD . . . C 2 69.935 33.172 -7.121 1 0 ? PN NAD 335 G 1 HETATM 25 O O1N NAD . . . C 2 71.175 33.812 -6.628 1 0 ? O1N NAD 335 G 1 HETATM 26 O O2N NAD . . . C 2 69.264 32.615 -5.926 1 0 ? O2N NAD 335 G 1 HETATM 27 O O5D NAD . . . C 2 70.307 31.987 -8.13 1 0 ? O5D NAD 335 G 1 HETATM 28 C C5D NAD . . . C 2 69.997 32.136 -9.529 1 0 ? C5D NAD 335 G 1 HETATM 29 C C4D NAD . . . C 2 71.221 31.831 -10.368 1 0 ? C4D NAD 335 G 1 HETATM 30 O O4D NAD . . . C 2 72.323 31.674 -9.479 1 0 ? O4D NAD 335 G 1 HETATM 31 C C3D NAD . . . C 2 71.165 30.539 -11.184 1 0 ? C3D NAD 335 G 1 HETATM 32 O O3D NAD . . . C 2 71.871 30.733 -12.403 1 0 ? O3D NAD 335 G 1 HETATM 33 C C2D NAD . . . C 2 71.932 29.551 -10.307 1 0 ? C2D NAD 335 G 1 HETATM 34 O O2D NAD . . . C 2 72.477 28.445 -11.004 1 0 ? O2D NAD 335 G 1 HETATM 35 C C1D NAD . . . C 2 73.008 30.453 -9.712 1 0 ? C1D NAD 335 G 1 HETATM 36 N N1N NAD . . . C 2 73.543 29.969 -8.407 1 0 ? N1N NAD 335 G 1 HETATM 37 C C2N NAD . . . C 2 72.713 30.012 -7.353 1 0 ? C2N NAD 335 G 1 HETATM 38 C C3N NAD . . . C 2 73.15 29.575 -6.11 1 0 ? C3N NAD 335 G 1 HETATM 39 C C7N NAD . . . C 2 72.143 29.666 -5.002 1 0 ? C7N NAD 335 G 1 HETATM 40 O O7N NAD . . . C 2 72.448 29.302 -3.874 1 0 ? O7N NAD 335 G 1 HETATM 41 N N7N NAD . . . C 2 70.924 30.156 -5.307 1 0 ? N7N NAD 335 G 1 HETATM 42 C C4N NAD . . . C 2 74.436 29.104 -5.983 1 0 ? C4N NAD 335 G 1 HETATM 43 C C5N NAD . . . C 2 75.255 29.076 -7.087 1 0 ? C5N NAD 335 G 1 HETATM 44 C C6N NAD . . . C 2 74.806 29.511 -8.303 1 0 ? C6N NAD 335 G 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 44 #