data_5L58 # _model_server_result.job_id LA-WlRoQYrSqEQcnwJlFhg _model_server_result.datetime_utc '2024-11-21 23:35:30' _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 5l58 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 5L58 # _exptl.entry_id 5L58 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 745.421 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _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 90 _cell.entry_id 5L58 _cell.length_a 72.166 _cell.length_b 72.166 _cell.length_c 179.829 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5L58 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _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 _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' 7_557 y,x,-z+2 0 1 0 1 0 0 0 0 -1 0 0 359.658 # _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 # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id NH2 _struct_conn.ptnr1_label_comp_id ARG _struct_conn.ptnr1_label_seq_id 314 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id ARG _struct_conn.ptnr1_auth_seq_id 314 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id O3X _struct_conn.ptnr2_label_comp_id NDP _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id NDP _struct_conn.ptnr2_auth_seq_id 501 _struct_conn.ptnr2_symmetry 1_555 _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 1.297 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C21 H30 N7 O17 P3' _chem_comp.formula_weight 745.421 _chem_comp.id NDP _chem_comp.mon_nstd_flag . _chem_comp.name 'NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' _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 NDP doub 315 n n PA O2A NDP sing 316 n n PA O5B NDP sing 317 n n PA O3 NDP sing 318 n n O2A HOA2 NDP sing 319 n n O5B C5B NDP sing 320 n n C5B C4B NDP sing 321 n n C5B H51A NDP sing 322 n n C5B H52A NDP sing 323 n n C4B O4B NDP sing 324 n n C4B C3B NDP sing 325 n n C4B H4B NDP sing 326 n n O4B C1B NDP sing 327 n n C3B O3B NDP sing 328 n n C3B C2B NDP sing 329 n n C3B H3B NDP sing 330 n n O3B HO3A NDP sing 331 n n C2B O2B NDP sing 332 n n C2B C1B NDP sing 333 n n C2B H2B NDP sing 334 n n O2B P2B NDP sing 335 n n C1B N9A NDP sing 336 n n C1B H1B NDP sing 337 n n N9A C8A NDP sing 338 n y N9A C4A NDP sing 339 n y C8A N7A NDP doub 340 n y C8A H8A NDP sing 341 n n N7A C5A NDP sing 342 n y C5A C6A NDP sing 343 n y C5A C4A NDP doub 344 n y C6A N6A NDP sing 345 n n C6A N1A NDP doub 346 n y N6A H61A NDP sing 347 n n N6A H62A NDP sing 348 n n N1A C2A NDP sing 349 n y C2A N3A NDP doub 350 n y C2A H2A NDP sing 351 n n N3A C4A NDP sing 352 n y O3 PN NDP sing 353 n n PN O1N NDP doub 354 n n PN O2N NDP sing 355 n n PN O5D NDP sing 356 n n O2N H21N NDP sing 357 n n O5D C5D NDP sing 358 n n C5D C4D NDP sing 359 n n C5D H51N NDP sing 360 n n C5D H52N NDP sing 361 n n C4D O4D NDP sing 362 n n C4D C3D NDP sing 363 n n C4D H4D NDP sing 364 n n O4D C1D NDP sing 365 n n C3D O3D NDP sing 366 n n C3D C2D NDP sing 367 n n C3D H3D NDP sing 368 n n O3D HO3N NDP sing 369 n n C2D O2D NDP sing 370 n n C2D C1D NDP sing 371 n n C2D H2D NDP sing 372 n n O2D HO2N NDP sing 373 n n C1D N1N NDP sing 374 n n C1D H1D NDP sing 375 n n N1N C2N NDP sing 376 n n N1N C6N NDP sing 377 n n C2N C3N NDP doub 378 n n C2N H2N NDP sing 379 n n C3N C7N NDP sing 380 n n C3N C4N NDP sing 381 n n C7N O7N NDP doub 382 n n C7N N7N NDP sing 383 n n N7N H71N NDP sing 384 n n N7N H72N NDP sing 385 n n C4N C5N NDP sing 386 n n C4N H41N NDP sing 387 n n C4N H42N NDP sing 388 n n C5N C6N NDP doub 389 n n C5N H5N NDP sing 390 n n C6N H6N NDP sing 391 n n P2B O1X NDP doub 392 n n P2B O2X NDP sing 393 n n P2B O3X NDP sing 394 n n O2X HOP2 NDP sing 395 n n O3X HOP3 NDP sing 396 n n # _atom_sites.entry_id 5L58 _atom_sites.fract_transf_matrix[1][1] 0.013857 _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] 0.013857 _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] 0.005561 _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 NDP A 1 501 501 NDP NDP . C 3 6MX A 1 502 1 6MX 04I . # 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 NDP . . . B 2 3.172 34.143 175.756 1 47.22 ? PA NDP 501 A 1 HETATM 2 O O1A NDP . . . B 2 3.468 33.146 176.822 1 37.54 ? O1A NDP 501 A 1 HETATM 3 O O2A NDP . . . B 2 2.612 35.495 176.086 1 42.93 ? O2A NDP 501 A 1 HETATM 4 O O5B NDP . . . B 2 2.248 33.427 174.603 1 49.9 ? O5B NDP 501 A 1 HETATM 5 C C5B NDP . . . B 2 2.918 32.243 174.333 1 45.74 ? C5B NDP 501 A 1 HETATM 6 C C4B NDP . . . B 2 2.003 31.344 173.552 1 40.63 ? C4B NDP 501 A 1 HETATM 7 O O4B NDP . . . B 2 1.858 30.091 174.227 1 34.95 ? O4B NDP 501 A 1 HETATM 8 C C3B NDP . . . B 2 0.623 32.019 173.445 1 43.99 ? C3B NDP 501 A 1 HETATM 9 O O3B NDP . . . B 2 0.532 32.744 172.258 1 47.01 ? O3B NDP 501 A 1 HETATM 10 C C2B NDP . . . B 2 -0.26 30.777 173.344 1 41.91 ? C2B NDP 501 A 1 HETATM 11 O O2B NDP . . . B 2 -0.186 30.179 172.155 1 46.05 ? O2B NDP 501 A 1 HETATM 12 C C1B NDP . . . B 2 0.461 29.894 174.433 1 37.46 ? C1B NDP 501 A 1 HETATM 13 N N9A NDP . . . B 2 0.151 30.329 175.811 1 42.54 ? N9A NDP 501 A 1 HETATM 14 C C8A NDP . . . B 2 1.001 30.966 176.735 1 39.36 ? C8A NDP 501 A 1 HETATM 15 N N7A NDP . . . B 2 0.412 31.234 177.916 1 34.52 ? N7A NDP 501 A 1 HETATM 16 C C5A NDP . . . B 2 -0.892 30.741 177.756 1 37.04 ? C5A NDP 501 A 1 HETATM 17 C C6A NDP . . . B 2 -1.996 30.716 178.622 1 37.12 ? C6A NDP 501 A 1 HETATM 18 N N6A NDP . . . B 2 -1.895 31.244 179.893 1 33.73 ? N6A NDP 501 A 1 HETATM 19 N N1A NDP . . . B 2 -3.189 30.172 178.24 1 40.98 ? N1A NDP 501 A 1 HETATM 20 C C2A NDP . . . B 2 -3.212 29.665 176.96 1 47.31 ? C2A NDP 501 A 1 HETATM 21 N N3A NDP . . . B 2 -2.256 29.614 176.017 1 49.4 ? N3A NDP 501 A 1 HETATM 22 C C4A NDP . . . B 2 -1.073 30.173 176.449 1 43.6 ? C4A NDP 501 A 1 HETATM 23 O O3 NDP . . . B 2 4.686 34.393 175.158 1 50.32 ? O3 NDP 501 A 1 HETATM 24 P PN NDP . . . B 2 4.596 35.347 173.888 1 45.26 ? PN NDP 501 A 1 HETATM 25 O O1N NDP . . . B 2 5.689 34.975 172.968 1 40.58 ? O1N NDP 501 A 1 HETATM 26 O O2N NDP . . . B 2 3.195 35.675 173.418 1 53.31 ? O2N NDP 501 A 1 HETATM 27 O O5D NDP . . . B 2 5.154 36.935 174.405 1 40.55 ? O5D NDP 501 A 1 HETATM 28 C C5D NDP . . . B 2 4.061 37.758 174.355 1 38.05 ? C5D NDP 501 A 1 HETATM 29 C C4D NDP . . . B 2 4.332 38.945 175.241 1 39.35 ? C4D NDP 501 A 1 HETATM 30 O O4D NDP . . . B 2 4.612 38.485 176.567 1 45.13 ? O4D NDP 501 A 1 HETATM 31 C C3D NDP . . . B 2 5.623 39.646 174.726 1 34.89 ? C3D NDP 501 A 1 HETATM 32 O O3D NDP . . . B 2 5.327 40.984 174.503 1 34.22 ? O3D NDP 501 A 1 HETATM 33 C C2D NDP . . . B 2 6.606 39.479 175.894 1 33.28 ? C2D NDP 501 A 1 HETATM 34 O O2D NDP . . . B 2 7.363 40.62 176.13 1 31.27 ? O2D NDP 501 A 1 HETATM 35 C C1D NDP . . . B 2 5.629 39.302 177.078 1 40.46 ? C1D NDP 501 A 1 HETATM 36 N N1N NDP . . . B 2 6.296 38.596 178.181 1 41.01 ? N1N NDP 501 A 1 HETATM 37 C C2N NDP . . . B 2 6.246 39.132 179.443 1 46.84 ? C2N NDP 501 A 1 HETATM 38 C C3N NDP . . . B 2 6.523 38.364 180.525 1 46 ? C3N NDP 501 A 1 HETATM 39 C C7N NDP . . . B 2 6.44 39.029 181.815 1 48.65 ? C7N NDP 501 A 1 HETATM 40 O O7N NDP . . . B 2 6.451 38.45 182.908 1 55.53 ? O7N NDP 501 A 1 HETATM 41 N N7N NDP . . . B 2 6.342 40.409 181.793 1 45.18 ? N7N NDP 501 A 1 HETATM 42 C C4N NDP . . . B 2 6.891 36.927 180.399 1 42.04 ? C4N NDP 501 A 1 HETATM 43 C C5N NDP . . . B 2 7.271 36.58 179.001 1 40.17 ? C5N NDP 501 A 1 HETATM 44 C C6N NDP . . . B 2 6.978 37.384 177.971 1 37.08 ? C6N NDP 501 A 1 HETATM 45 P P2B NDP . . . B 2 -1.568 29.021 171.847 1 55.08 ? P2B NDP 501 A 1 HETATM 46 O O1X NDP . . . B 2 -0.78 28.03 171.047 1 48.96 ? O1X NDP 501 A 1 HETATM 47 O O2X NDP . . . B 2 -2.014 28.602 173.252 1 64.8 ? O2X NDP 501 A 1 HETATM 48 O O3X NDP . . . B 2 -2.462 29.965 171.092 1 41.77 ? O3X NDP 501 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 48 #