data_3JD4 # _model_server_result.job_id lArjM0nBgUECJmCqWy8DUw _model_server_result.datetime_utc '2024-11-01 04:37:51' _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 3jd4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":603}' # _entry.id 3JD4 # _exptl.entry_id 3JD4 _exptl.method 'ELECTRON MICROSCOPY' # _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 12 _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 3JD4 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3JD4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X _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 G N N ? 2 I N N ? 2 J N N ? 2 L N N ? 2 M N N ? 2 N N N ? 2 P N N ? 2 R N N ? 2 S N N ? 2 U N N ? 2 V N N ? 2 W N N # _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 285 n n PA O2A NAI sing 286 n n PA O5B NAI sing 287 n n PA O3 NAI sing 288 n n O2A HOA2 NAI sing 289 n n O5B C5B NAI sing 290 n n C5B C4B NAI sing 291 n n C5B H51A NAI sing 292 n n C5B H52A NAI sing 293 n n C4B O4B NAI sing 294 n n C4B C3B NAI sing 295 n n C4B H4B NAI sing 296 n n O4B C1B NAI sing 297 n n C3B O3B NAI sing 298 n n C3B C2B NAI sing 299 n n C3B H3B NAI sing 300 n n O3B HO3A NAI sing 301 n n C2B O2B NAI sing 302 n n C2B C1B NAI sing 303 n n C2B H2B NAI sing 304 n n O2B HO2A NAI sing 305 n n C1B N9A NAI sing 306 n n C1B H1B NAI sing 307 n n N9A C8A NAI sing 308 n y N9A C4A NAI sing 309 n y C8A N7A NAI doub 310 n y C8A H8A NAI sing 311 n n N7A C5A NAI sing 312 n y C5A C6A NAI sing 313 n y C5A C4A NAI doub 314 n y C6A N6A NAI sing 315 n n C6A N1A NAI doub 316 n y N6A H61A NAI sing 317 n n N6A H62A NAI sing 318 n n N1A C2A NAI sing 319 n y C2A N3A NAI doub 320 n y C2A H2A NAI sing 321 n n N3A C4A NAI sing 322 n y O3 PN NAI sing 323 n n PN O1N NAI sing 324 n n PN O2N NAI doub 325 n n PN O5D NAI sing 326 n n O1N HO1N NAI sing 327 n n O5D C5D NAI sing 328 n n C5D C4D NAI sing 329 n n C5D H51N NAI sing 330 n n C5D H52N NAI sing 331 n n C4D O4D NAI sing 332 n n C4D C3D NAI sing 333 n n C4D H4D NAI sing 334 n n O4D C1D NAI sing 335 n n C3D O3D NAI sing 336 n n C3D C2D NAI sing 337 n n C3D H3D NAI sing 338 n n O3D HO3N NAI sing 339 n n C2D O2D NAI sing 340 n n C2D C1D NAI sing 341 n n C2D H2D NAI sing 342 n n O2D HO2N NAI sing 343 n n C1D N1N NAI sing 344 n n C1D H1D NAI sing 345 n n N1N C2N NAI sing 346 n n N1N C6N NAI sing 347 n n C2N C3N NAI doub 348 n n C2N H2N NAI sing 349 n n C3N C7N NAI sing 350 n n C3N C4N NAI sing 351 n n C7N O7N NAI doub 352 n n C7N N7N NAI sing 353 n n N7N H71N NAI sing 354 n n N7N H72N NAI sing 355 n n C4N C5N NAI sing 356 n n C4N H4N NAI sing 357 n n C4N H42N NAI sing 358 n n C5N C6N NAI doub 359 n n C5N H5N NAI sing 360 n n C6N H6N NAI sing 361 n n # _atom_sites.entry_id 3JD4 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 G 2 NAI A 1 601 601 NAI NAI . H 3 GTP A 1 602 602 GTP GTP . I 2 NAI A 1 603 603 NAI NAI . J 2 NAI B 1 602 601 NAI NAI . K 3 GTP B 1 603 602 GTP GTP . L 2 NAI B 1 601 603 NAI NAI . M 2 NAI C 1 601 603 NAI NAI . N 2 NAI C 1 602 601 NAI NAI . O 3 GTP C 1 603 602 GTP GTP . P 2 NAI D 1 601 601 NAI NAI . Q 3 GTP D 1 602 602 GTP GTP . R 2 NAI D 1 603 603 NAI NAI . S 2 NAI E 1 602 601 NAI NAI . T 3 GTP E 1 603 602 GTP GTP . U 2 NAI E 1 601 603 NAI NAI . V 2 NAI F 1 601 603 NAI NAI . W 2 NAI F 1 602 601 NAI NAI . X 3 GTP F 1 603 602 GTP GTP . # 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 . . . I 2 69.134 71.145 53.63 1 82.96 ? PA NAI 603 A 1 HETATM 2 O O1A NAI . . . I 2 70.178 70.098 53.35 1 51.25 ? O1A NAI 603 A 1 HETATM 3 O O2A NAI . . . I 2 68.382 71.802 52.502 1 71.06 ? O2A NAI 603 A 1 HETATM 4 O O5B NAI . . . I 2 68.067 70.531 54.657 1 70.51 ? O5B NAI 603 A 1 HETATM 5 C C5B NAI . . . I 2 68.07 69.126 54.874 1 66.31 ? C5B NAI 603 A 1 HETATM 6 C C4B NAI . . . I 2 66.763 68.726 55.526 1 63.84 ? C4B NAI 603 A 1 HETATM 7 O O4B NAI . . . I 2 66.488 69.58 56.634 1 60.04 ? O4B NAI 603 A 1 HETATM 8 C C3B NAI . . . I 2 65.623 68.886 54.541 1 63.64 ? C3B NAI 603 A 1 HETATM 9 O O3B NAI . . . I 2 64.937 67.641 54.388 1 69.8 ? O3B NAI 603 A 1 HETATM 10 C C2B NAI . . . I 2 64.694 69.9 55.163 1 63.72 ? C2B NAI 603 A 1 HETATM 11 O O2B NAI . . . I 2 63.342 69.464 55.016 1 67.28 ? O2B NAI 603 A 1 HETATM 12 C C1B NAI . . . I 2 65.106 69.919 56.62 1 59.9 ? C1B NAI 603 A 1 HETATM 13 N N9A NAI . . . I 2 64.871 71.26 57.188 1 50.95 ? N9A NAI 603 A 1 HETATM 14 C C8A NAI . . . I 2 65.311 72.426 56.695 1 53.37 ? C8A NAI 603 A 1 HETATM 15 N N7A NAI . . . I 2 64.897 73.46 57.466 1 45.05 ? N7A NAI 603 A 1 HETATM 16 C C5A NAI . . . I 2 64.17 72.948 58.47 1 42.89 ? C5A NAI 603 A 1 HETATM 17 C C6A NAI . . . I 2 63.438 73.473 59.635 1 45.3 ? C6A NAI 603 A 1 HETATM 18 N N6A NAI . . . I 2 63.392 74.792 59.901 1 45.98 ? N6A NAI 603 A 1 HETATM 19 N N1A NAI . . . I 2 62.813 72.599 60.435 1 41.94 ? N1A NAI 603 A 1 HETATM 20 C C2A NAI . . . I 2 62.846 71.284 60.19 1 41.95 ? C2A NAI 603 A 1 HETATM 21 N N3A NAI . . . I 2 63.49 70.735 59.154 1 45.12 ? N3A NAI 603 A 1 HETATM 22 C C4A NAI . . . I 2 64.154 71.502 58.275 1 50.4 ? C4A NAI 603 A 1 HETATM 23 O O3 NAI . . . I 2 69.815 72.287 54.517 1 70.67 ? O3 NAI 603 A 1 HETATM 24 P PN NAI . . . I 2 70.837 71.809 55.648 1 65.61 ? PN NAI 603 A 1 HETATM 25 O O1N NAI . . . I 2 72.141 71.442 54.998 1 62.03 ? O1N NAI 603 A 1 HETATM 26 O O2N NAI . . . I 2 70.126 70.826 56.533 1 63.77 ? O2N NAI 603 A 1 HETATM 27 O O5D NAI . . . I 2 71.041 73.143 56.5 1 64.49 ? O5D NAI 603 A 1 HETATM 28 C C5D NAI . . . I 2 70.534 73.153 57.822 1 57.83 ? C5D NAI 603 A 1 HETATM 29 C C4D NAI . . . I 2 71.457 73.96 58.705 1 60.91 ? C4D NAI 603 A 1 HETATM 30 O O4D NAI . . . I 2 70.965 73.895 60.035 1 62.89 ? O4D NAI 603 A 1 HETATM 31 C C3D NAI . . . I 2 72.838 73.349 58.696 1 50.2 ? C3D NAI 603 A 1 HETATM 32 O O3D NAI . . . I 2 73.752 74.278 58.119 1 48.82 ? O3D NAI 603 A 1 HETATM 33 C C2D NAI . . . I 2 73.208 73.158 60.14 1 51.53 ? C2D NAI 603 A 1 HETATM 34 O O2D NAI . . . I 2 74.289 74.039 60.41 1 52.61 ? O2D NAI 603 A 1 HETATM 35 C C1D NAI . . . I 2 72.021 73.629 60.948 1 53.76 ? C1D NAI 603 A 1 HETATM 36 N N1N NAI . . . I 2 71.579 72.582 61.847 1 53.13 ? N1N NAI 603 A 1 HETATM 37 C C2N NAI . . . I 2 71.414 72.827 63.14 1 57.66 ? C2N NAI 603 A 1 HETATM 38 C C3N NAI . . . I 2 70.977 71.839 64.006 1 54.92 ? C3N NAI 603 A 1 HETATM 39 C C7N NAI . . . I 2 70.807 72.114 65.464 1 54.64 ? C7N NAI 603 A 1 HETATM 40 O O7N NAI . . . I 2 71.334 73.096 65.955 1 53.19 ? O7N NAI 603 A 1 HETATM 41 N N7N NAI . . . I 2 70.086 71.256 66.183 1 55.75 ? N7N NAI 603 A 1 HETATM 42 C C4N NAI . . . I 2 70.665 70.452 63.523 1 53.69 ? C4N NAI 603 A 1 HETATM 43 C C5N NAI . . . I 2 70.888 70.328 62.095 1 53.71 ? C5N NAI 603 A 1 HETATM 44 C C6N NAI . . . I 2 71.321 71.394 61.326 1 54.16 ? C6N NAI 603 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 41 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 44 #