data_3TVX # _model_server_result.job_id xgCU4TuDGkWE_Vic9ovGtQ _model_server_result.datetime_utc '2024-10-15 08:17:11' _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 3tvx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":902}' # _entry.id 3TVX # _exptl.entry_id 3TVX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 278.307 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3,7-DIMETHYL-1-(5-OXOHEXYL)-3,7-DIHYDRO-1H-PURINE-2,6-DIONE _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 90 _cell.angle_gamma 90 _cell.entry_id 3TVX _cell.length_a 104.938 _cell.length_b 104.938 _cell.length_c 163.652 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3TVX _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E 1 1 B,F,G,H,I,J 2 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 ? 4 E N N ? 4 H 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 A NE2 HIS 92 A HIS 376 1_555 C ZN ZN . A ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc2 A NE2 HIS 128 A HIS 412 1_555 C ZN ZN . A ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc3 A OD2 ASP 129 A ASP 413 1_555 C ZN ZN . A ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc4 A OD1 ASP 129 A ASP 413 1_555 D MG MG . A MG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc5 A OD1 ASP 246 A ASP 530 1_555 C ZN ZN . A ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc6 B NE2 HIS 92 B HIS 376 1_555 F ZN ZN . B ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? metalc ? metalc7 B NE2 HIS 128 B HIS 412 1_555 F ZN ZN . B ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc8 B OD2 ASP 129 B ASP 413 1_555 F ZN ZN . B ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? metalc ? metalc9 B OD1 ASP 129 B ASP 413 1_555 G MG MG . B MG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc10 B OD1 ASP 246 B ASP 530 1_555 F ZN ZN . B ZN 900 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.275 ? # _chem_comp.formula 'C13 H18 N4 O3' _chem_comp.formula_weight 278.307 _chem_comp.id PNX _chem_comp.mon_nstd_flag . _chem_comp.name 3,7-DIMETHYL-1-(5-OXOHEXYL)-3,7-DIHYDRO-1H-PURINE-2,6-DIONE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms PENTOXIFYLLINE # 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 CAA CAM PNX sing 258 n n CAA HAA1 PNX sing 259 n n CAA HAA2 PNX sing 260 n n CAA HAA3 PNX sing 261 n n CAM OAD PNX doub 262 n n CAM CAJ PNX sing 263 n n CAJ CAH PNX sing 264 n n CAJ HAJ1 PNX sing 265 n n CAJ HAJ2 PNX sing 266 n n CAH CAI PNX sing 267 n n CAH HAH1 PNX sing 268 n n CAH HAH2 PNX sing 269 n n CAI CAK PNX sing 270 n n CAI HAI1 PNX sing 271 n n CAI HAI2 PNX sing 272 n n CAK N1 PNX sing 273 n n CAK HAK1 PNX sing 274 n n CAK HAK2 PNX sing 275 n n N1 C6 PNX sing 276 n y N1 C2 PNX sing 277 n y C6 O6 PNX doub 278 n n C6 C5 PNX sing 279 n y C5 N7 PNX sing 280 n y C5 C4 PNX doub 281 n y N7 CAB PNX sing 282 n n N7 C8 PNX sing 283 n y CAB HAB1 PNX sing 284 n n CAB HAB2 PNX sing 285 n n CAB HAB3 PNX sing 286 n n C8 N9 PNX doub 287 n y C8 H8 PNX sing 288 n n N9 C4 PNX sing 289 n y C4 N3 PNX sing 290 n y N3 CAC PNX sing 291 n n N3 C2 PNX sing 292 n y CAC HAC1 PNX sing 293 n n CAC HAC2 PNX sing 294 n n CAC HAC3 PNX sing 295 n n C2 O2 PNX doub 296 n n # _atom_sites.entry_id 3TVX _atom_sites.fract_transf_matrix[1][1] 0.009529 _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] 0.009529 _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] 0.006111 _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 ZN A 1 900 900 ZN ZN . D 3 MG A 1 901 901 MG MG . E 4 PNX A 1 902 902 PNX LIG . F 2 ZN B 1 900 900 ZN ZN . G 3 MG B 1 901 901 MG MG . H 4 PNX B 1 902 902 PNX LIG . I 5 SO4 B 1 903 903 SO4 SO4 . J 5 SO4 B 1 904 904 SO4 SO4 . # 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 C CAA PNX . . . H 4 13.059 45.928 -24.754 1 94.63 ? CAA PNX 902 B 1 HETATM 2 C CAM PNX . . . H 4 13.374 46.076 -23.283 1 94.98 ? CAM PNX 902 B 1 HETATM 3 O OAD PNX . . . H 4 13.282 47.178 -22.764 1 95.93 ? OAD PNX 902 B 1 HETATM 4 C CAJ PNX . . . H 4 13.804 44.875 -22.471 1 94.41 ? CAJ PNX 902 B 1 HETATM 5 C CAH PNX . . . H 4 13.842 45.13 -20.958 1 93.93 ? CAH PNX 902 B 1 HETATM 6 C CAI PNX . . . H 4 12.441 45.105 -20.336 1 93.39 ? CAI PNX 902 B 1 HETATM 7 C CAK PNX . . . H 4 11.801 43.721 -20.482 1 93.05 ? CAK PNX 902 B 1 HETATM 8 N N1 PNX . . . H 4 10.353 43.833 -20.676 1 92.65 ? N1 PNX 902 B 1 HETATM 9 C C6 PNX . . . H 4 9.569 43.777 -19.561 1 93.19 ? C6 PNX 902 B 1 HETATM 10 O O6 PNX . . . H 4 10.054 43.645 -18.448 1 92.99 ? O6 PNX 902 B 1 HETATM 11 C C5 PNX . . . H 4 8.183 43.881 -19.757 1 93.81 ? C5 PNX 902 B 1 HETATM 12 N N7 PNX . . . H 4 7.125 43.873 -18.895 1 94.12 ? N7 PNX 902 B 1 HETATM 13 C CAB PNX . . . H 4 7.107 43.744 -17.435 1 93.77 ? CAB PNX 902 B 1 HETATM 14 C C8 PNX . . . H 4 6 44.01 -19.633 1 94.18 ? C8 PNX 902 B 1 HETATM 15 N N9 PNX . . . H 4 6.329 44.106 -20.938 1 93.82 ? N9 PNX 902 B 1 HETATM 16 C C4 PNX . . . H 4 7.674 44.027 -21.055 1 93.76 ? C4 PNX 902 B 1 HETATM 17 N N3 PNX . . . H 4 8.492 44.074 -22.143 1 93.09 ? N3 PNX 902 B 1 HETATM 18 C CAC PNX . . . H 4 7.954 44.225 -23.494 1 92.97 ? CAC PNX 902 B 1 HETATM 19 C C2 PNX . . . H 4 9.828 43.974 -21.925 1 92.62 ? C2 PNX 902 B 1 HETATM 20 O O2 PNX . . . H 4 10.558 44.02 -22.907 1 91.98 ? O2 PNX 902 B 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 298 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 20 #