data_4LD4 # _model_server_result.job_id Lz1MvO4SSQMAQ-tycbx5xQ _model_server_result.datetime_utc '2025-06-28 19:13:27' _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 4ld4 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":202}' # _entry.id 4LD4 # _exptl.entry_id 4LD4 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 111.102 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 6-AMINOPYRIMIDIN-2(1H)-ONE _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 4LD4 _cell.length_a 38.35 _cell.length_b 73.85 _cell.length_c 110.38 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4LD4 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 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,E,F,G _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 3 _struct_asym.id E _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 182 A CYS 180 1_555 A SG CYS 191 A CYS 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc1 A ND1 HIS 79 A HIS 77 1_555 C ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? metalc ? metalc2 A SG CYS 114 A CYS 112 1_555 C ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.367 ? metalc ? metalc3 A SG CYS 117 A CYS 115 1_555 C ZN ZN . A ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc4 B ND1 HIS 79 B HIS 77 1_555 D ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? metalc ? metalc5 B SG CYS 114 B CYS 112 1_555 D ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc6 B SG CYS 117 B CYS 115 1_555 D ZN ZN . B ZN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? # _chem_comp.formula 'C4 H5 N3 O' _chem_comp.formula_weight 111.102 _chem_comp.id CYT _chem_comp.mon_nstd_flag . _chem_comp.name 6-AMINOPYRIMIDIN-2(1H)-ONE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms CYTOSINE # 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 N3 C4 CYT sing 83 n y N3 C2 CYT sing 84 n y N3 HN3 CYT sing 85 n n C4 N4 CYT sing 86 n n C4 C5 CYT doub 87 n y N1 C2 CYT sing 88 n y N1 C6 CYT doub 89 n y C2 O2 CYT doub 90 n n N4 HN41 CYT sing 91 n n N4 HN42 CYT sing 92 n n C5 C6 CYT sing 93 n y C5 H5 CYT sing 94 n n C6 H6 CYT sing 95 n n # _atom_sites.entry_id 4LD4 _atom_sites.fract_transf_matrix[1][1] 0.026076 _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] 0.013541 _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] 0.00906 _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 1 201 506 ZN ZN . D 2 ZN B 1 201 507 ZN ZN . E 3 CYT B 1 202 1 CYT DRG . F 4 HOH A 1 301 3 HOH HOH . F 4 HOH A 2 302 7 HOH HOH . F 4 HOH A 3 303 9 HOH HOH . F 4 HOH A 4 304 13 HOH HOH . F 4 HOH A 5 305 14 HOH HOH . F 4 HOH A 6 306 18 HOH HOH . F 4 HOH A 7 307 19 HOH HOH . F 4 HOH A 8 308 23 HOH HOH . F 4 HOH A 9 309 24 HOH HOH . F 4 HOH A 10 310 26 HOH HOH . F 4 HOH A 11 311 27 HOH HOH . F 4 HOH A 12 312 28 HOH HOH . F 4 HOH A 13 313 29 HOH HOH . F 4 HOH A 14 314 30 HOH HOH . F 4 HOH A 15 315 31 HOH HOH . F 4 HOH A 16 316 32 HOH HOH . F 4 HOH A 17 317 34 HOH HOH . F 4 HOH A 18 318 35 HOH HOH . F 4 HOH A 19 319 36 HOH HOH . F 4 HOH A 20 320 37 HOH HOH . F 4 HOH A 21 321 39 HOH HOH . G 4 HOH B 1 301 1 HOH HOH . G 4 HOH B 2 302 2 HOH HOH . G 4 HOH B 3 303 4 HOH HOH . G 4 HOH B 4 304 5 HOH HOH . G 4 HOH B 5 305 6 HOH HOH . G 4 HOH B 6 306 8 HOH HOH . G 4 HOH B 7 307 10 HOH HOH . G 4 HOH B 8 308 11 HOH HOH . G 4 HOH B 9 309 12 HOH HOH . G 4 HOH B 10 310 15 HOH HOH . G 4 HOH B 11 311 16 HOH HOH . G 4 HOH B 12 312 17 HOH HOH . G 4 HOH B 13 313 20 HOH HOH . G 4 HOH B 14 314 21 HOH HOH . G 4 HOH B 15 315 22 HOH HOH . G 4 HOH B 16 316 25 HOH HOH . G 4 HOH B 17 317 33 HOH HOH . G 4 HOH B 18 318 38 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 N N3 CYT . . . E 3 32.19 37.889 26.836 1 36.42 ? N3 CYT 202 B 1 HETATM 2 C C4 CYT . . . E 3 33.214 36.936 26.709 1 35.09 ? C4 CYT 202 B 1 HETATM 3 N N1 CYT . . . E 3 33.771 39.432 27.69 1 35.68 ? N1 CYT 202 B 1 HETATM 4 C C2 CYT . . . E 3 32.493 39.149 27.353 1 35.98 ? C2 CYT 202 B 1 HETATM 5 O O2 CYT . . . E 3 31.623 39.974 27.484 1 36.42 ? O2 CYT 202 B 1 HETATM 6 N N4 CYT . . . E 3 32.912 35.749 26.236 1 32.88 ? N4 CYT 202 B 1 HETATM 7 C C5 CYT . . . E 3 34.532 37.228 27.062 1 35.2 ? C5 CYT 202 B 1 HETATM 8 C C6 CYT . . . E 3 34.81 38.494 27.568 1 35.6 ? C6 CYT 202 B 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 355 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 8 #