data_7DN9 # _model_server_result.job_id cpEnexYvVKHR7gc4EuSt0A _model_server_result.datetime_utc '2024-11-25 20:26:58' _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 7dn9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":401}' # _entry.id 7DN9 # _exptl.entry_id 7DN9 _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 104.8 _cell.angle_gamma 90 _cell.entry_id 7DN9 _cell.length_a 104.711 _cell.length_b 105.576 _cell.length_c 105.839 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7DN9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # 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 PISA dimeric 2 author_and_software_defined_assembly 3 PISA dimeric 2 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,I,J,K 1 1 C,D,L,M,N 2 1 E,F,O,P,Q 3 1 G,H,R,S,T 4 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 I N N ? 3 L N N ? 3 O N N ? 3 R 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 metalc ? metalc1 B OG1 THR 32 B THR 48 1_555 J MG MG . B MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.86 ? metalc ? metalc2 J MG MG . B MG 201 1_555 K O1B GDP . B GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc3 M MG MG . D MG 201 1_555 N O1B GDP . D GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc4 F OG1 THR 32 F THR 48 1_555 P MG MG . F MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.96 ? metalc ? metalc5 P MG MG . F MG 201 1_555 Q O1B GDP . F GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc6 H OG1 THR 32 H THR 48 1_555 S MG MG . H MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.728 ? metalc ? metalc7 S MG MG . H MG 201 1_555 T O3B GDP . H GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.753 ? metalc ? metalc8 S MG MG . H MG 201 1_555 T O1B GDP . H GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? # _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 280 n n PA O2A NAD sing 281 n n PA O5B NAD sing 282 n n PA O3 NAD sing 283 n n O2A HOA2 NAD sing 284 n n O5B C5B NAD sing 285 n n C5B C4B NAD sing 286 n n C5B H51A NAD sing 287 n n C5B H52A NAD sing 288 n n C4B O4B NAD sing 289 n n C4B C3B NAD sing 290 n n C4B H4B NAD sing 291 n n O4B C1B NAD sing 292 n n C3B O3B NAD sing 293 n n C3B C2B NAD sing 294 n n C3B H3B NAD sing 295 n n O3B HO3A NAD sing 296 n n C2B O2B NAD sing 297 n n C2B C1B NAD sing 298 n n C2B H2B NAD sing 299 n n O2B HO2A NAD sing 300 n n C1B N9A NAD sing 301 n n C1B H1B NAD sing 302 n n N9A C8A NAD sing 303 n y N9A C4A NAD sing 304 n y C8A N7A NAD doub 305 n y C8A H8A NAD sing 306 n n N7A C5A NAD sing 307 n y C5A C6A NAD sing 308 n y C5A C4A NAD doub 309 n y C6A N6A NAD sing 310 n n C6A N1A NAD doub 311 n y N6A H61A NAD sing 312 n n N6A H62A NAD sing 313 n n N1A C2A NAD sing 314 n y C2A N3A NAD doub 315 n y C2A H2A NAD sing 316 n n N3A C4A NAD sing 317 n y O3 PN NAD sing 318 n n PN O1N NAD doub 319 n n PN O2N NAD sing 320 n n PN O5D NAD sing 321 n n O5D C5D NAD sing 322 n n C5D C4D NAD sing 323 n n C5D H51N NAD sing 324 n n C5D H52N NAD sing 325 n n C4D O4D NAD sing 326 n n C4D C3D NAD sing 327 n n C4D H4D NAD sing 328 n n O4D C1D NAD sing 329 n n C3D O3D NAD sing 330 n n C3D C2D NAD sing 331 n n C3D H3D NAD sing 332 n n O3D HO3N NAD sing 333 n n C2D O2D NAD sing 334 n n C2D C1D NAD sing 335 n n C2D H2D NAD sing 336 n n O2D HO2N NAD sing 337 n n C1D N1N NAD sing 338 n n C1D H1D NAD sing 339 n n N1N C2N NAD sing 340 n y N1N C6N NAD doub 341 n y C2N C3N NAD doub 342 n y C2N H2N NAD sing 343 n n C3N C7N NAD sing 344 n n C3N C4N NAD sing 345 n y C7N O7N NAD doub 346 n n C7N N7N NAD sing 347 n n N7N H71N NAD sing 348 n n N7N H72N NAD sing 349 n n C4N C5N NAD doub 350 n y C4N H4N NAD sing 351 n n C5N C6N NAD sing 352 n y C5N H5N NAD sing 353 n n C6N H6N NAD sing 354 n n # _atom_sites.entry_id 7DN9 _atom_sites.fract_transf_matrix[1][1] 0.00955 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002524 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009472 _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] 0.009773 _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 I 3 NAD A 1 401 401 NAD NAD . J 4 MG B 1 201 201 MG MG . K 5 GDP B 1 202 202 GDP GDP . L 3 NAD C 1 401 401 NAD NAD . M 4 MG D 1 201 201 MG MG . N 5 GDP D 1 202 202 GDP GDP . O 3 NAD E 1 401 401 NAD NAD . P 4 MG F 1 201 201 MG MG . Q 5 GDP F 1 202 202 GDP GDP . R 3 NAD G 1 401 401 NAD NAD . S 4 MG H 1 201 201 MG MG . T 5 GDP H 1 202 202 GDP GDP . # 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 . . . R 3 -0.962 40.279 -22.204 1 89.7 ? PA NAD 401 G 1 HETATM 2 O O1A NAD . . . R 3 -1.501 40.91 -23.445 1 60.54 ? O1A NAD 401 G 1 HETATM 3 O O2A NAD . . . R 3 0.231 40.904 -21.558 1 74.42 ? O2A NAD 401 G 1 HETATM 4 O O5B NAD . . . R 3 -0.658 38.729 -22.482 1 76.52 ? O5B NAD 401 G 1 HETATM 5 C C5B NAD . . . R 3 0.698 38.312 -22.779 1 66.62 ? C5B NAD 401 G 1 HETATM 6 C C4B NAD . . . R 3 1.079 37.195 -21.838 1 78.43 ? C4B NAD 401 G 1 HETATM 7 O O4B NAD . . . R 3 2.332 36.613 -22.288 1 87.86 ? O4B NAD 401 G 1 HETATM 8 C C3B NAD . . . R 3 1.328 37.608 -20.379 1 73.04 ? C3B NAD 401 G 1 HETATM 9 O O3B NAD . . . R 3 0.981 36.545 -19.501 1 68.4 ? O3B NAD 401 G 1 HETATM 10 C C2B NAD . . . R 3 2.846 37.795 -20.368 1 69.59 ? C2B NAD 401 G 1 HETATM 11 O O2B NAD . . . R 3 3.417 37.788 -19.077 1 50.26 ? O2B NAD 401 G 1 HETATM 12 C C1B NAD . . . R 3 3.244 36.593 -21.214 1 75.72 ? C1B NAD 401 G 1 HETATM 13 N N9A NAD . . . R 3 4.595 36.666 -21.755 1 71.03 ? N9A NAD 401 G 1 HETATM 14 C C8A NAD . . . R 3 5.312 37.805 -22.025 1 60.36 ? C8A NAD 401 G 1 HETATM 15 N N7A NAD . . . R 3 6.504 37.565 -22.511 1 59.87 ? N7A NAD 401 G 1 HETATM 16 C C5A NAD . . . R 3 6.58 36.181 -22.569 1 71.22 ? C5A NAD 401 G 1 HETATM 17 C C6A NAD . . . R 3 7.597 35.305 -22.997 1 73.34 ? C6A NAD 401 G 1 HETATM 18 N N6A NAD . . . R 3 8.774 35.709 -23.465 1 66.15 ? N6A NAD 401 G 1 HETATM 19 N N1A NAD . . . R 3 7.348 33.976 -22.923 1 76.15 ? N1A NAD 401 G 1 HETATM 20 C C2A NAD . . . R 3 6.161 33.573 -22.451 1 75.33 ? C2A NAD 401 G 1 HETATM 21 N N3A NAD . . . R 3 5.135 34.301 -22.022 1 77.68 ? N3A NAD 401 G 1 HETATM 22 C C4A NAD . . . R 3 5.408 35.614 -22.106 1 76.35 ? C4A NAD 401 G 1 HETATM 23 O O3 NAD . . . R 3 -2.132 40.158 -21.112 1 84.45 ? O3 NAD 401 G 1 HETATM 24 P PN NAD . . . R 3 -2.532 41.016 -19.816 1 68.86 ? PN NAD 401 G 1 HETATM 25 O O1N NAD . . . R 3 -1.285 41.347 -19.065 1 48.44 ? O1N NAD 401 G 1 HETATM 26 O O2N NAD . . . R 3 -3.629 40.304 -19.095 1 59.54 ? O2N NAD 401 G 1 HETATM 27 O O5D NAD . . . R 3 -3.115 42.347 -20.492 1 62.24 ? O5D NAD 401 G 1 HETATM 28 C C5D NAD . . . R 3 -4.139 42.219 -21.508 1 66.54 ? C5D NAD 401 G 1 HETATM 29 C C4D NAD . . . R 3 -4.311 43.551 -22.195 1 59.3 ? C4D NAD 401 G 1 HETATM 30 O O4D NAD . . . R 3 -4.365 44.594 -21.203 1 48.53 ? O4D NAD 401 G 1 HETATM 31 C C3D NAD . . . R 3 -3.183 43.993 -23.135 1 51.66 ? C3D NAD 401 G 1 HETATM 32 O O3D NAD . . . R 3 -3.24 43.357 -24.406 1 53.64 ? O3D NAD 401 G 1 HETATM 33 C C2D NAD . . . R 3 -3.416 45.508 -23.183 1 57.3 ? C2D NAD 401 G 1 HETATM 34 O O2D NAD . . . R 3 -4.312 45.866 -24.222 1 50.99 ? O2D NAD 401 G 1 HETATM 35 C C1D NAD . . . R 3 -4.029 45.836 -21.818 1 54.35 ? C1D NAD 401 G 1 HETATM 36 N N1N NAD . . . R 3 -3.063 46.541 -20.925 1 52.03 ? N1N NAD 401 G 1 HETATM 37 C C2N NAD . . . R 3 -2.25 45.822 -20.083 1 47.13 ? C2N NAD 401 G 1 HETATM 38 C C3N NAD . . . R 3 -1.348 46.475 -19.25 1 43.04 ? C3N NAD 401 G 1 HETATM 39 C C7N NAD . . . R 3 -0.505 45.67 -18.294 1 44.22 ? C7N NAD 401 G 1 HETATM 40 O O7N NAD . . . R 3 0.221 46.253 -17.492 1 39.15 ? O7N NAD 401 G 1 HETATM 41 N N7N NAD . . . R 3 -0.594 44.349 -18.357 1 48.94 ? N7N NAD 401 G 1 HETATM 42 C C4N NAD . . . R 3 -1.245 47.858 -19.321 1 47.71 ? C4N NAD 401 G 1 HETATM 43 C C5N NAD . . . R 3 -2.065 48.564 -20.17 1 51.71 ? C5N NAD 401 G 1 HETATM 44 C C6N NAD . . . R 3 -2.977 47.89 -20.95 1 53.01 ? C6N NAD 401 G 1 # _model_server_stats.io_time_ms 28 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 44 #