data_8Y1Q # _model_server_result.job_id ZkcZHzBma75Oyhiv3djeBg _model_server_result.datetime_utc '2024-11-24 02:38:30' _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 8y1q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":201}' # _entry.id 8Y1Q # _exptl.entry_id 8Y1Q _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE-5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 3 _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 8Y1Q _cell.length_a 61.26 _cell.length_b 61.26 _cell.length_c 112.66 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8Y1Q _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall 'P 4w' _symmetry.space_group_name_H-M 'P 41' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 F N N ? 2 G N N # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id I _struct_conn.ptnr1_label_atom_id O _struct_conn.ptnr1_label_comp_id HOH _struct_conn.ptnr1_label_seq_id . _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id HOH _struct_conn.ptnr1_auth_seq_id 302 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id H _struct_conn.ptnr2_label_atom_id MG _struct_conn.ptnr2_label_comp_id MG _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id C _struct_conn.ptnr2_auth_comp_id MG _struct_conn.ptnr2_auth_seq_id 202 _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 2.304 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C9 H13 N2 O8 P' _chem_comp.formula_weight 308.182 _chem_comp.id DU _chem_comp.mon_nstd_flag y _chem_comp.name "2'-DEOXYURIDINE-5'-MONOPHOSPHATE" _chem_comp.type 'dna linking' _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 OP3 P DU sing 70 n n OP3 HOP3 DU sing 71 n n P OP1 DU doub 72 n n P OP2 DU sing 73 n n P O5' DU sing 74 n n OP2 HOP2 DU sing 75 n n O5' C5' DU sing 76 n n C5' C4' DU sing 77 n n C5' H5' DU sing 78 n n C5' "H5''" DU sing 79 n n C4' O4' DU sing 80 n n C4' C3' DU sing 81 n n C4' H4' DU sing 82 n n O4' C1' DU sing 83 n n C3' O3' DU sing 84 n n C3' C2' DU sing 85 n n C3' H3' DU sing 86 n n O3' HO3' DU sing 87 n n C2' C1' DU sing 88 n n C2' H2' DU sing 89 n n C2' "H2''" DU sing 90 n n C1' N1 DU sing 91 n n C1' H1' DU sing 92 n n N1 C2 DU sing 93 n n N1 C6 DU sing 94 n n C2 O2 DU doub 95 n n C2 N3 DU sing 96 n n N3 C4 DU sing 97 n n N3 H3 DU sing 98 n n C4 O4 DU doub 99 n n C4 C5 DU sing 100 n n C5 C6 DU doub 101 n n C5 H5 DU sing 102 n n C6 H6 DU sing 103 n n # _atom_sites.entry_id 8Y1Q _atom_sites.fract_transf_matrix[1][1] 0.016324 _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] 0.016324 _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] 0.008876 _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 D 2 DU A 1 201 201 DU DU . E 3 MG A 1 202 1 MG MG . F 2 DU B 1 201 201 DU DU . G 2 DU C 1 201 201 DU DU . H 3 MG C 1 202 2 MG MG . I 4 HOH A 1 301 4 HOH HOH . I 4 HOH A 2 302 7 HOH HOH . I 4 HOH A 3 303 5 HOH HOH . I 4 HOH A 4 304 2 HOH HOH . J 4 HOH B 1 301 1 HOH HOH . J 4 HOH B 2 302 8 HOH HOH . J 4 HOH B 3 303 6 HOH HOH . J 4 HOH B 4 304 9 HOH HOH . K 4 HOH C 1 301 3 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 O OP3 DU . . . D 2 5.065 38.897 -12.928 1 98.65 ? OP3 DU 201 A 1 HETATM 2 P P DU . . . D 2 5.127 40.476 -13.184 1 105.13 ? P DU 201 A 1 HETATM 3 O OP1 DU . . . D 2 6.392 40.971 -12.584 1 94.84 ? OP1 DU 201 A 1 HETATM 4 O OP2 DU . . . D 2 4.848 40.746 -14.618 1 96.93 ? OP2 DU 201 A 1 HETATM 5 O O5' DU . . . D 2 3.921 41.051 -12.316 1 107.83 ? O5' DU 201 A 1 HETATM 6 C C5' DU . . . D 2 4.071 41.263 -10.897 1 93.82 ? C5' DU 201 A 1 HETATM 7 C C4' DU . . . D 2 3.06 42.272 -10.401 1 97.52 ? C4' DU 201 A 1 HETATM 8 O O4' DU . . . D 2 1.722 41.778 -10.625 1 95.68 ? O4' DU 201 A 1 HETATM 9 C C3' DU . . . D 2 3.128 42.557 -8.905 1 93.3 ? C3' DU 201 A 1 HETATM 10 O O3' DU . . . D 2 4.058 43.612 -8.641 1 91.82 ? O3' DU 201 A 1 HETATM 11 C C2' DU . . . D 2 1.711 42.994 -8.58 1 86.87 ? C2' DU 201 A 1 HETATM 12 C C1' DU . . . D 2 0.851 42.254 -9.604 1 93.75 ? C1' DU 201 A 1 HETATM 13 N N1 DU . . . D 2 0.121 41.101 -9.057 1 86.34 ? N1 DU 201 A 1 HETATM 14 C C2 DU . . . D 2 -1.235 41.245 -8.848 1 86.37 ? C2 DU 201 A 1 HETATM 15 O O2 DU . . . D 2 -1.84 42.272 -9.097 1 90.79 ? O2 DU 201 A 1 HETATM 16 N N3 DU . . . D 2 -1.861 40.134 -8.332 1 71.13 ? N3 DU 201 A 1 HETATM 17 C C4 DU . . . D 2 -1.276 38.925 -8.015 1 79.35 ? C4 DU 201 A 1 HETATM 18 O O4 DU . . . D 2 -1.974 38.017 -7.558 1 67.58 ? O4 DU 201 A 1 HETATM 19 C C5 DU . . . D 2 0.131 38.86 -8.262 1 83.16 ? C5 DU 201 A 1 HETATM 20 C C6 DU . . . D 2 0.767 39.924 -8.763 1 78.07 ? C6 DU 201 A 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 46 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 342 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 20 #