data_5L4E # _model_server_result.job_id Zlw4dhqWo50P9ktPIJqw2g _model_server_result.datetime_utc '2025-01-22 07:03:54' _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 5l4e # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":402}' # _entry.id 5L4E # _exptl.entry_id 5L4E _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 242.338 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-ethyl-5-[(2R)-pentan-2-yl]-2-thioxodihydropyrimidine-4,6(1H,5H)-dione _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 101.88 _cell.angle_gamma 90 _cell.entry_id 5L4E _cell.length_a 182.025 _cell.length_b 134.581 _cell.length_c 159.018 _cell.Z_PDB 20 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5L4E _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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,E,F,G,H,I,J,K,L,M,N,O,P,Q _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 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id K _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 disulf ? disulf1 A SG CYS 33 A CYS 33 1_555 A SG CYS 246 A CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? disulf ? disulf2 B SG CYS 33 B CYS 33 1_555 B SG CYS 246 B CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf3 C SG CYS 33 C CYS 33 1_555 C SG CYS 246 C CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf4 D SG CYS 33 D CYS 33 1_555 D SG CYS 246 D CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf5 E SG CYS 33 E CYS 33 1_555 E SG CYS 246 E CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? # _chem_comp.formula 'C11 H18 N2 O2 S' _chem_comp.formula_weight 242.338 _chem_comp.id EDP _chem_comp.mon_nstd_flag . _chem_comp.name 5-ethyl-5-[(2R)-pentan-2-yl]-2-thioxodihydropyrimidine-4,6(1H,5H)-dione _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Thiopental # 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 C6 C1 EDP sing 120 n n C2 C1 EDP sing 121 n n C1 C14 EDP sing 122 n n C1 C12 EDP sing 123 n n N3 C2 EDP sing 124 n n C2 O8 EDP doub 125 n n C4 N3 EDP sing 126 n n N3 HN3 EDP sing 127 n n S9 C4 EDP doub 128 n n C4 N5 EDP sing 129 n n N5 C6 EDP sing 130 n n N5 HN5 EDP sing 131 n n C6 O7 EDP doub 132 n n C12 C13 EDP sing 133 n n C12 H12 EDP sing 134 n n C12 H12A EDP sing 135 n n C13 H13 EDP sing 136 n n C13 H13A EDP sing 137 n n C13 H13B EDP sing 138 n n C15 C14 EDP sing 139 n n C14 C16 EDP sing 140 n n C14 H14 EDP sing 141 n n C15 H15 EDP sing 142 n n C15 H15A EDP sing 143 n n C15 H15B EDP sing 144 n n C16 C17 EDP sing 145 n n C16 H16 EDP sing 146 n n C16 H16A EDP sing 147 n n C18 C17 EDP sing 148 n n C17 H17 EDP sing 149 n n C17 H17A EDP sing 150 n n C18 H18 EDP sing 151 n n C18 H18A EDP sing 152 n n C18 H18B EDP sing 153 n n # _atom_sites.entry_id 5L4E _atom_sites.fract_transf_matrix[1][1] 0.005494 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001156 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00743 _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] 0.006426 _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 F 2 D12 A 1 401 318 D12 LMT . G 3 CL A 1 402 319 CL CL . H 3 CL B 1 401 318 CL CL . I 3 CL C 1 401 318 CL CL . J 3 CL D 1 401 318 CL CL . K 4 EDP D 1 402 1 EDP EDP . L 3 CL E 1 401 318 CL CL . M 5 HOH A 1 501 328 HOH HOH . M 5 HOH A 2 502 329 HOH HOH . M 5 HOH A 3 503 337 HOH HOH . M 5 HOH A 4 504 322 HOH HOH . M 5 HOH A 5 505 341 HOH HOH . M 5 HOH A 6 506 334 HOH HOH . N 5 HOH B 1 501 341 HOH HOH . N 5 HOH B 2 502 319 HOH HOH . N 5 HOH B 3 503 339 HOH HOH . N 5 HOH B 4 504 335 HOH HOH . O 5 HOH C 1 501 324 HOH HOH . O 5 HOH C 2 502 334 HOH HOH . P 5 HOH D 1 501 332 HOH HOH . P 5 HOH D 2 502 319 HOH HOH . P 5 HOH D 3 503 323 HOH HOH . P 5 HOH D 4 504 331 HOH HOH . P 5 HOH D 5 505 333 HOH HOH . Q 5 HOH E 1 501 322 HOH HOH . Q 5 HOH E 2 502 332 HOH HOH . Q 5 HOH E 3 503 327 HOH HOH . Q 5 HOH E 4 504 337 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 C C1 EDP . . . K 4 64.552 -26.453 57.46 0 142.11 ? C1 EDP 402 D 1 HETATM 2 C C2 EDP . . . K 4 63.624 -25.33 57.028 1 138.68 ? C2 EDP 402 D 1 HETATM 3 N N3 EDP . . . K 4 62.865 -25.535 55.906 1 134.19 ? N3 EDP 402 D 1 HETATM 4 C C4 EDP . . . K 4 62.851 -26.643 55.118 1 133.09 ? C4 EDP 402 D 1 HETATM 5 N N5 EDP . . . K 4 63.674 -27.66 55.486 1 135.82 ? N5 EDP 402 D 1 HETATM 6 C C6 EDP . . . K 4 64.509 -27.693 56.571 1 140.47 ? C6 EDP 402 D 1 HETATM 7 O O7 EDP . . . K 4 65.14 -28.71 56.827 1 141.08 ? O7 EDP 402 D 1 HETATM 8 O O8 EDP . . . K 4 63.581 -24.26 57.617 1 139.06 ? O8 EDP 402 D 1 HETATM 9 S S9 EDP . . . K 4 61.86 -26.755 53.773 1 132.5 ? S9 EDP 402 D 1 HETATM 10 C C12 EDP . . . K 4 65.925 -25.737 57.352 0.46 143.59 ? C12 EDP 402 D 1 HETATM 11 C C13 EDP . . . K 4 67.137 -26.61 57.501 0.93 143.95 ? C13 EDP 402 D 1 HETATM 12 C C14 EDP . . . K 4 64.209 -26.978 58.905 0.06 144.64 ? C14 EDP 402 D 1 HETATM 13 C C15 EDP . . . K 4 62.708 -26.968 59.183 0.89 146.97 ? C15 EDP 402 D 1 HETATM 14 C C16 EDP . . . K 4 64.92 -26.285 60.091 1 143.54 ? C16 EDP 402 D 1 HETATM 15 C C17 EDP . . . K 4 65.441 -27.248 61.145 1 142.57 ? C17 EDP 402 D 1 HETATM 16 C C18 EDP . . . K 4 66.308 -26.583 62.184 1 143.13 ? C18 EDP 402 D 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 16 #