data_2DLD # _model_server_result.job_id teBbnv1FyXEjjTXKFeYiBA _model_server_result.datetime_utc '2024-12-14 19:30:01' _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 2dld # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 2DLD # _exptl.entry_id 2DLD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 665.441 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '1,4-DIHYDRONICOTINAMIDE 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 113.2 _cell.angle_gamma 90 _cell.entry_id 2DLD _cell.length_a 86.2 _cell.length_b 62.1 _cell.length_c 77.4 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2DLD _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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,E,F _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 ? 2 C N N ? 2 E 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 OD1 ASP 176 A ASP 176 1_555 C N3A NAI . A NAI 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.916 ? covale ? covale2 E C5N NAI . B NAI 401 1_555 F N1 OXM . B OXM 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? # _chem_comp.formula 'C21 H29 N7 O14 P2' _chem_comp.formula_weight 665.441 _chem_comp.id NAI _chem_comp.mon_nstd_flag . _chem_comp.name '1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms NADH # 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 NAI doub 235 n n PA O2A NAI sing 236 n n PA O5B NAI sing 237 n n PA O3 NAI sing 238 n n O2A HOA2 NAI sing 239 n n O5B C5B NAI sing 240 n n C5B C4B NAI sing 241 n n C5B H51A NAI sing 242 n n C5B H52A NAI sing 243 n n C4B O4B NAI sing 244 n n C4B C3B NAI sing 245 n n C4B H4B NAI sing 246 n n O4B C1B NAI sing 247 n n C3B O3B NAI sing 248 n n C3B C2B NAI sing 249 n n C3B H3B NAI sing 250 n n O3B HO3A NAI sing 251 n n C2B O2B NAI sing 252 n n C2B C1B NAI sing 253 n n C2B H2B NAI sing 254 n n O2B HO2A NAI sing 255 n n C1B N9A NAI sing 256 n n C1B H1B NAI sing 257 n n N9A C8A NAI sing 258 n y N9A C4A NAI sing 259 n y C8A N7A NAI doub 260 n y C8A H8A NAI sing 261 n n N7A C5A NAI sing 262 n y C5A C6A NAI sing 263 n y C5A C4A NAI doub 264 n y C6A N6A NAI sing 265 n n C6A N1A NAI doub 266 n y N6A H61A NAI sing 267 n n N6A H62A NAI sing 268 n n N1A C2A NAI sing 269 n y C2A N3A NAI doub 270 n y C2A H2A NAI sing 271 n n N3A C4A NAI sing 272 n y O3 PN NAI sing 273 n n PN O1N NAI sing 274 n n PN O2N NAI doub 275 n n PN O5D NAI sing 276 n n O1N HO1N NAI sing 277 n n O5D C5D NAI sing 278 n n C5D C4D NAI sing 279 n n C5D H51N NAI sing 280 n n C5D H52N NAI sing 281 n n C4D O4D NAI sing 282 n n C4D C3D NAI sing 283 n n C4D H4D NAI sing 284 n n O4D C1D NAI sing 285 n n C3D O3D NAI sing 286 n n C3D C2D NAI sing 287 n n C3D H3D NAI sing 288 n n O3D HO3N NAI sing 289 n n C2D O2D NAI sing 290 n n C2D C1D NAI sing 291 n n C2D H2D NAI sing 292 n n O2D HO2N NAI sing 293 n n C1D N1N NAI sing 294 n n C1D H1D NAI sing 295 n n N1N C2N NAI sing 296 n n N1N C6N NAI sing 297 n n C2N C3N NAI doub 298 n n C2N H2N NAI sing 299 n n C3N C7N NAI sing 300 n n C3N C4N NAI sing 301 n n C7N O7N NAI doub 302 n n C7N N7N NAI sing 303 n n N7N H71N NAI sing 304 n n N7N H72N NAI sing 305 n n C4N C5N NAI sing 306 n n C4N H4N NAI sing 307 n n C4N H42N NAI sing 308 n n C5N C6N NAI doub 309 n n C5N H5N NAI sing 310 n n C6N H6N NAI sing 311 n n # _atom_sites.entry_id 2DLD _atom_sites.fract_transf_matrix[1][1] 0.011601 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.004972 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016103 _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] 0.014057 _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 NAI A 1 401 401 NAI NAD . D 3 OXM A 1 402 402 OXM OXM . E 2 NAI B 1 401 401 NAI NAD . F 3 OXM B 1 402 402 OXM OXM . # 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 NAI . . . E 2 37.134 12.4 19.649 1 79.5 ? PA NAI 401 B 1 HETATM 2 O O1A NAI . . . E 2 37.747 11.021 19.666 1 79.1 ? O1A NAI 401 B 1 HETATM 3 O O2A NAI . . . E 2 37.864 13.478 18.839 1 79.32 ? O2A NAI 401 B 1 HETATM 4 O O5B NAI . . . E 2 36.946 12.898 21.159 1 77.41 ? O5B NAI 401 B 1 HETATM 5 C C5B NAI . . . E 2 37.449 14.27 21.551 1 74 ? C5B NAI 401 B 1 HETATM 6 C C4B NAI . . . E 2 38.181 14.1 22.813 1 71.89 ? C4B NAI 401 B 1 HETATM 7 O O4B NAI . . . E 2 37.657 12.795 23.443 1 69.19 ? O4B NAI 401 B 1 HETATM 8 C C3B NAI . . . E 2 39.728 13.845 22.775 1 71.26 ? C3B NAI 401 B 1 HETATM 9 O O3B NAI . . . E 2 40.383 15.007 23.477 1 71.52 ? O3B NAI 401 B 1 HETATM 10 C C2B NAI . . . E 2 40.022 12.529 23.432 1 70.46 ? C2B NAI 401 B 1 HETATM 11 O O2B NAI . . . E 2 41.148 12.344 24.155 1 70.32 ? O2B NAI 401 B 1 HETATM 12 C C1B NAI . . . E 2 38.716 12.379 24.216 1 68.65 ? C1B NAI 401 B 1 HETATM 13 N N9A NAI . . . E 2 38.459 11.1 24.745 1 67.12 ? N9A NAI 401 B 1 HETATM 14 C C8A NAI . . . E 2 38.694 9.824 24.272 1 66.68 ? C8A NAI 401 B 1 HETATM 15 N N7A NAI . . . E 2 38.387 8.84 25.095 1 65.74 ? N7A NAI 401 B 1 HETATM 16 C C5A NAI . . . E 2 37.942 9.413 26.207 1 65.74 ? C5A NAI 401 B 1 HETATM 17 C C6A NAI . . . E 2 37.415 8.809 27.439 1 65.96 ? C6A NAI 401 B 1 HETATM 18 N N6A NAI . . . E 2 37.303 7.528 27.683 1 65.4 ? N6A NAI 401 B 1 HETATM 19 N N1A NAI . . . E 2 37.022 9.76 28.35 1 66.58 ? N1A NAI 401 B 1 HETATM 20 C C2A NAI . . . E 2 37.098 11.091 28.21 1 67.18 ? C2A NAI 401 B 1 HETATM 21 N N3A NAI . . . E 2 37.588 11.706 27.054 1 66.33 ? N3A NAI 401 B 1 HETATM 22 C C4A NAI . . . E 2 37.989 10.821 26.059 1 66.44 ? C4A NAI 401 B 1 HETATM 23 O O3 NAI . . . E 2 35.647 12.296 19.203 1 78.26 ? O3 NAI 401 B 1 HETATM 24 P PN NAI . . . E 2 34.53 13.254 18.394 1 76.15 ? PN NAI 401 B 1 HETATM 25 O O1N NAI . . . E 2 35.199 13.707 17.172 1 75.2 ? O1N NAI 401 B 1 HETATM 26 O O2N NAI . . . E 2 33.957 14.213 19.352 1 74.47 ? O2N NAI 401 B 1 HETATM 27 O O5D NAI . . . E 2 33.417 12.182 18.051 1 74.83 ? O5D NAI 401 B 1 HETATM 28 C C5D NAI . . . E 2 31.993 12.237 18.128 1 73.91 ? C5D NAI 401 B 1 HETATM 29 C C4D NAI . . . E 2 31.385 10.928 18.354 1 73.93 ? C4D NAI 401 B 1 HETATM 30 O O4D NAI . . . E 2 30.428 10.687 17.134 1 72.85 ? O4D NAI 401 B 1 HETATM 31 C C3D NAI . . . E 2 32.248 9.627 18.279 1 73.64 ? C3D NAI 401 B 1 HETATM 32 O O3D NAI . . . E 2 32.768 9.397 19.531 1 73.69 ? O3D NAI 401 B 1 HETATM 33 C C2D NAI . . . E 2 31.517 8.553 17.523 1 73.21 ? C2D NAI 401 B 1 HETATM 34 O O2D NAI . . . E 2 31.36 7.314 18.044 1 73.24 ? O2D NAI 401 B 1 HETATM 35 C C1D NAI . . . E 2 30.248 9.268 17.016 1 71.37 ? C1D NAI 401 B 1 HETATM 36 N N1N NAI . . . E 2 29.503 8.829 15.751 1 68.44 ? N1N NAI 401 B 1 HETATM 37 C C2N NAI . . . E 2 28.116 9.003 15.821 1 65.71 ? C2N NAI 401 B 1 HETATM 38 C C3N NAI . . . E 2 27.448 8.587 14.698 1 63.08 ? C3N NAI 401 B 1 HETATM 39 C C7N NAI . . . E 2 25.914 8.879 14.904 1 60.65 ? C7N NAI 401 B 1 HETATM 40 O O7N NAI . . . E 2 25.207 9.003 13.916 1 59.53 ? O7N NAI 401 B 1 HETATM 41 N N7N NAI . . . E 2 25.504 9.035 16.178 1 58.18 ? N7N NAI 401 B 1 HETATM 42 C C4N NAI . . . E 2 27.975 8.032 13.525 1 63.46 ? C4N NAI 401 B 1 HETATM 43 C C5N NAI . . . E 2 29.393 7.899 13.586 1 64.8 ? C5N NAI 401 B 1 HETATM 44 C C6N NAI . . . E 2 30.125 8.266 14.682 1 66.67 ? C6N NAI 401 B 1 # _model_server_stats.io_time_ms 45 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 44 #