data_5YVS # _model_server_result.job_id IS8klhOdl-pBeS0TpngG9w _model_server_result.datetime_utc '2024-11-28 12:15:19' _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 5yvs # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":502}' # _entry.id 5YVS # _exptl.entry_id 5YVS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 745.421 _entity.id 3 _entity.src_method nat _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 5YVS _cell.length_a 57.92 _cell.length_b 104.84 _cell.length_c 129.36 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YVS _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _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 _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' 3_655 -x+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 57.92 0 64.68 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 A OD1 ASP 213 A ASP 204 1_555 B MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc2 A NE2 HIS 217 A HIS 208 1_555 B MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.491 ? metalc ? metalc3 A NE2 HIS 282 A HIS 273 1_555 B MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.222 ? metalc ? metalc4 A NE2 HIS 297 A HIS 288 1_555 B MN MN . A MN 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? # _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 237 n n PA O2A NDP sing 238 n n PA O5B NDP sing 239 n n PA O3 NDP sing 240 n n O2A HOA2 NDP sing 241 n n O5B C5B NDP sing 242 n n C5B C4B NDP sing 243 n n C5B H51A NDP sing 244 n n C5B H52A NDP sing 245 n n C4B O4B NDP sing 246 n n C4B C3B NDP sing 247 n n C4B H4B NDP sing 248 n n O4B C1B NDP sing 249 n n C3B O3B NDP sing 250 n n C3B C2B NDP sing 251 n n C3B H3B NDP sing 252 n n O3B HO3A NDP sing 253 n n C2B O2B NDP sing 254 n n C2B C1B NDP sing 255 n n C2B H2B NDP sing 256 n n O2B P2B NDP sing 257 n n C1B N9A NDP sing 258 n n C1B H1B NDP sing 259 n n N9A C8A NDP sing 260 n y N9A C4A NDP sing 261 n y C8A N7A NDP doub 262 n y C8A H8A NDP sing 263 n n N7A C5A NDP sing 264 n y C5A C6A NDP sing 265 n y C5A C4A NDP doub 266 n y C6A N6A NDP sing 267 n n C6A N1A NDP doub 268 n y N6A H61A NDP sing 269 n n N6A H62A NDP sing 270 n n N1A C2A NDP sing 271 n y C2A N3A NDP doub 272 n y C2A H2A NDP sing 273 n n N3A C4A NDP sing 274 n y O3 PN NDP sing 275 n n PN O1N NDP doub 276 n n PN O2N NDP sing 277 n n PN O5D NDP sing 278 n n O2N H21N NDP sing 279 n n O5D C5D NDP sing 280 n n C5D C4D NDP sing 281 n n C5D H51N NDP sing 282 n n C5D H52N NDP sing 283 n n C4D O4D NDP sing 284 n n C4D C3D NDP sing 285 n n C4D H4D NDP sing 286 n n O4D C1D NDP sing 287 n n C3D O3D NDP sing 288 n n C3D C2D NDP sing 289 n n C3D H3D NDP sing 290 n n O3D HO3N NDP sing 291 n n C2D O2D NDP sing 292 n n C2D C1D NDP sing 293 n n C2D H2D NDP sing 294 n n O2D HO2N NDP sing 295 n n C1D N1N NDP sing 296 n n C1D H1D NDP sing 297 n n N1N C2N NDP sing 298 n n N1N C6N NDP sing 299 n n C2N C3N NDP doub 300 n n C2N H2N NDP sing 301 n n C3N C7N NDP sing 302 n n C3N C4N NDP sing 303 n n C7N O7N NDP doub 304 n n C7N N7N NDP sing 305 n n N7N H71N NDP sing 306 n n N7N H72N NDP sing 307 n n C4N C5N NDP sing 308 n n C4N H41N NDP sing 309 n n C4N H42N NDP sing 310 n n C5N C6N NDP doub 311 n n C5N H5N NDP sing 312 n n C6N H6N NDP sing 313 n n P2B O1X NDP doub 314 n n P2B O2X NDP sing 315 n n P2B O3X NDP sing 316 n n O2X HOP2 NDP sing 317 n n O3X HOP3 NDP sing 318 n n # _atom_sites.entry_id 5YVS _atom_sites.fract_transf_matrix[1][1] 0.017265 _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] 0.009538 _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] 0.00773 _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 MN A 1 501 1 MN MN . C 3 NDP A 1 502 1 NDP NDP . D 4 HOH A 1 601 1 HOH HOH . D 4 HOH A 2 602 9 HOH HOH . D 4 HOH A 3 603 5 HOH HOH . D 4 HOH A 4 604 7 HOH HOH . D 4 HOH A 5 605 3 HOH HOH . D 4 HOH A 6 606 4 HOH HOH . D 4 HOH A 7 607 8 HOH HOH . D 4 HOH A 8 608 6 HOH HOH . D 4 HOH A 9 609 2 HOH HOH . # 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 . . . C 3 22.081 13.934 56.575 1 60.93 ? PA NDP 502 A 1 HETATM 2 O O1A NDP . . . C 3 23.131 14.723 55.894 1 66.1 -1 O1A NDP 502 A 1 HETATM 3 O O2A NDP . . . C 3 20.647 14.368 56.478 1 72.46 ? O2A NDP 502 A 1 HETATM 4 O O5B NDP . . . C 3 22.478 13.895 58.187 1 69.92 ? O5B NDP 502 A 1 HETATM 5 C C5B NDP . . . C 3 23.468 12.91 58.327 1 65.7 ? C5B NDP 502 A 1 HETATM 6 C C4B NDP . . . C 3 23.588 12.563 59.782 1 67.54 ? C4B NDP 502 A 1 HETATM 7 O O4B NDP . . . C 3 24.748 11.784 59.981 1 72.58 ? O4B NDP 502 A 1 HETATM 8 C C3B NDP . . . C 3 23.707 13.867 60.582 1 62.54 ? C3B NDP 502 A 1 HETATM 9 O O3B NDP . . . C 3 23.267 13.639 61.873 1 58.39 ? O3B NDP 502 A 1 HETATM 10 C C2B NDP . . . C 3 25.24 14.11 60.581 1 67.02 ? C2B NDP 502 A 1 HETATM 11 O O2B NDP . . . C 3 25.712 14.729 61.682 1 70.25 ? O2B NDP 502 A 1 HETATM 12 C C1B NDP . . . C 3 25.767 12.629 60.551 1 66.52 ? C1B NDP 502 A 1 HETATM 13 N N9A NDP . . . C 3 26.938 12.499 59.696 1 56.05 ? N9A NDP 502 A 1 HETATM 14 C C8A NDP . . . C 3 27.118 12.964 58.381 1 50.62 ? C8A NDP 502 A 1 HETATM 15 N N7A NDP . . . C 3 28.329 12.667 57.874 1 52.93 ? N7A NDP 502 A 1 HETATM 16 C C5A NDP . . . C 3 28.96 11.968 58.92 1 53.43 ? C5A NDP 502 A 1 HETATM 17 C C6A NDP . . . C 3 30.234 11.383 59.03 1 65.8 ? C6A NDP 502 A 1 HETATM 18 N N6A NDP . . . C 3 31.136 11.432 57.977 1 72.37 ? N6A NDP 502 A 1 HETATM 19 N N1A NDP . . . C 3 30.617 10.742 60.177 1 71.62 ? N1A NDP 502 A 1 HETATM 20 C C2A NDP . . . C 3 29.672 10.73 61.181 1 69.02 ? C2A NDP 502 A 1 HETATM 21 N N3A NDP . . . C 3 28.434 11.236 61.225 1 58.44 ? N3A NDP 502 A 1 HETATM 22 C C4A NDP . . . C 3 28.098 11.86 60.057 1 52.18 ? C4A NDP 502 A 1 HETATM 23 O O3 NDP . . . C 3 22.28 12.443 55.905 1 67.29 ? O3 NDP 502 A 1 HETATM 24 P PN NDP . . . C 3 21.889 12.411 54.368 1 53.83 ? PN NDP 502 A 1 HETATM 25 O O1N NDP . . . C 3 22.891 13.219 53.652 1 59.51 -1 O1N NDP 502 A 1 HETATM 26 O O2N NDP . . . C 3 21.463 11.057 53.843 1 70.13 ? O2N NDP 502 A 1 HETATM 27 O O5D NDP . . . C 3 20.474 13.307 54.174 1 57.4 ? O5D NDP 502 A 1 HETATM 28 C C5D NDP . . . C 3 20.439 13.584 52.832 1 60.81 ? C5D NDP 502 A 1 HETATM 29 C C4D NDP . . . C 3 19.493 14.672 52.636 1 58.82 ? C4D NDP 502 A 1 HETATM 30 O O4D NDP . . . C 3 19.51 14.988 51.253 1 56.17 ? O4D NDP 502 A 1 HETATM 31 C C3D NDP . . . C 3 18.099 14.11 52.985 1 62.71 ? C3D NDP 502 A 1 HETATM 32 O O3D NDP . . . C 3 17.309 15.134 53.509 1 61.45 ? O3D NDP 502 A 1 HETATM 33 C C2D NDP . . . C 3 17.579 13.657 51.627 1 61.07 ? C2D NDP 502 A 1 HETATM 34 O O2D NDP . . . C 3 16.208 13.822 51.489 1 59.47 ? O2D NDP 502 A 1 HETATM 35 C C1D NDP . . . C 3 18.283 14.662 50.663 1 58.15 ? C1D NDP 502 A 1 HETATM 36 N N1N NDP . . . C 3 18.597 14.088 49.328 1 64.96 ? N1N NDP 502 A 1 HETATM 37 C C2N NDP . . . C 3 18.94 14.988 48.345 1 63.41 ? C2N NDP 502 A 1 HETATM 38 C C3N NDP . . . C 3 19.326 14.58 47.113 1 68.27 ? C3N NDP 502 A 1 HETATM 39 C C7N NDP . . . C 3 19.676 15.645 46.171 1 69.47 ? C7N NDP 502 A 1 HETATM 40 O O7N NDP . . . C 3 19.628 16.856 46.43 1 72.35 ? O7N NDP 502 A 1 HETATM 41 N N7N NDP . . . C 3 20.093 15.257 44.912 1 73.67 ? N7N NDP 502 A 1 HETATM 42 C C4N NDP . . . C 3 19.401 13.13 46.742 1 76.52 ? C4N NDP 502 A 1 HETATM 43 C C5N NDP . . . C 3 18.97 12.23 47.85 1 74.87 ? C5N NDP 502 A 1 HETATM 44 C C6N NDP . . . C 3 18.6 12.697 49.045 1 68.1 ? C6N NDP 502 A 1 HETATM 45 P P2B NDP . . . C 3 25.275 16.53 61.787 1 71.2 ? P2B NDP 502 A 1 HETATM 46 O O1X NDP . . . C 3 25.299 16.817 60.318 1 74.17 ? O1X NDP 502 A 1 HETATM 47 O O2X NDP . . . C 3 23.908 16.517 62.48 1 76.93 -1 O2X NDP 502 A 1 HETATM 48 O O3X NDP . . . C 3 26.455 16.988 62.601 1 71.63 ? O3X NDP 502 A 1 HETATM 49 H H51A NDP . . . C 3 23.287 12.131 57.778 1 78.84 ? H51A NDP 502 A 1 HETATM 50 H H52A NDP . . . C 3 24.317 13.266 58.021 1 78.84 ? H52A NDP 502 A 1 HETATM 51 H H4B NDP . . . C 3 22.824 12.032 60.056 1 81.05 ? H4B NDP 502 A 1 HETATM 52 H H3B NDP . . . C 3 23.259 14.617 60.16 1 75.05 ? H3B NDP 502 A 1 HETATM 53 H HO3A NDP . . . C 3 22.695 14.247 62.03 1 70.07 ? HO3A NDP 502 A 1 HETATM 54 H H2B NDP . . . C 3 25.472 14.511 59.729 1 80.43 ? H2B NDP 502 A 1 HETATM 55 H H1B NDP . . . C 3 26.016 12.32 61.437 1 79.82 ? H1B NDP 502 A 1 HETATM 56 H H8A NDP . . . C 3 26.449 13.431 57.935 1 60.75 ? H8A NDP 502 A 1 HETATM 57 H H61A NDP . . . C 3 31.909 11.066 58.065 1 86.84 ? H61A NDP 502 A 1 HETATM 58 H H62A NDP . . . C 3 30.913 11.827 57.246 1 86.84 ? H62A NDP 502 A 1 HETATM 59 H H2A NDP . . . C 3 29.954 10.292 61.951 1 82.83 ? H2A NDP 502 A 1 HETATM 60 H H51N NDP . . . C 3 20.116 12.815 52.338 1 72.97 ? H51N NDP 502 A 1 HETATM 61 H H52N NDP . . . C 3 21.313 13.777 52.458 1 72.97 ? H52N NDP 502 A 1 HETATM 62 H H4D NDP . . . C 3 19.742 15.437 53.177 1 70.58 ? H4D NDP 502 A 1 HETATM 63 H H3D NDP . . . C 3 18.181 13.354 53.588 1 75.25 ? H3D NDP 502 A 1 HETATM 64 H HO3N NDP . . . C 3 16.682 14.747 53.933 1 73.74 ? HO3N NDP 502 A 1 HETATM 65 H H2D NDP . . . C 3 17.847 12.745 51.433 1 73.28 ? H2D NDP 502 A 1 HETATM 66 H HO2N NDP . . . C 3 15.894 13.04 51.388 1 71.36 ? HO2N NDP 502 A 1 HETATM 67 H H1D NDP . . . C 3 17.769 15.475 50.539 1 69.79 ? H1D NDP 502 A 1 HETATM 68 H H2N NDP . . . C 3 18.906 15.893 48.556 1 76.09 ? H2N NDP 502 A 1 HETATM 69 H H71N NDP . . . C 3 20.133 14.421 44.714 1 88.41 ? H71N NDP 502 A 1 HETATM 70 H H72N NDP . . . C 3 20.314 15.832 44.311 1 88.41 ? H72N NDP 502 A 1 HETATM 71 H H41N NDP . . . C 3 18.851 12.952 45.962 1 91.83 ? H41N NDP 502 A 1 HETATM 72 H H42N NDP . . . C 3 20.308 12.909 46.481 1 91.83 ? H42N NDP 502 A 1 HETATM 73 H H5N NDP . . . C 3 18.96 11.312 47.698 1 89.84 ? H5N NDP 502 A 1 HETATM 74 H H6N NDP . . . C 3 18.331 12.134 49.735 1 81.72 ? H6N NDP 502 A 1 # _model_server_stats.io_time_ms 71 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 74 #