data_1PEO # _model_server_result.job_id W-ktjxn0ICXZEMXlIX2YXg _model_server_result.datetime_utc '2024-11-23 23:36:59' _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 1peo # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":716}' # _entry.id 1PEO # _exptl.entry_id 1PEO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 467.157 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE" _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 1PEO _cell.length_a 98.938 _cell.length_b 98.938 _cell.length_c 289.151 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1PEO _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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' 7_556 y,x,-z+1 0 1 0 1 0 0 0 0 -1 0 0 289.151 # _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 disulf ? disulf1 A SG CYS 178 A CYS 178 1_555 A SG CYS 415 A CYS 415 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc1 B MG MG . A MG 715 1_555 C O1G DCP . A DCP 716 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.94 ? metalc ? metalc2 B MG MG . A MG 715 1_555 C O2A DCP . A DCP 716 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.153 ? metalc ? metalc3 B MG MG . A MG 715 1_555 C O1B DCP . A DCP 716 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc4 B MG MG . A MG 715 1_555 C O3G DCP . A DCP 716 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? # _chem_comp.formula 'C9 H16 N3 O13 P3' _chem_comp.formula_weight 467.157 _chem_comp.id DCP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE" _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 N1 C2 DCP sing 83 n n N1 C6 DCP sing 84 n n N1 C1' DCP sing 85 n n C2 N3 DCP sing 86 n n C2 O2 DCP doub 87 n n N3 C4 DCP doub 88 n n C4 C5 DCP sing 89 n n C4 N4 DCP sing 90 n n C5 C6 DCP doub 91 n n C5 H5 DCP sing 92 n n C6 H6 DCP sing 93 n n N4 HN41 DCP sing 94 n n N4 HN42 DCP sing 95 n n C1' C2' DCP sing 96 n n C1' O4' DCP sing 97 n n C1' H1' DCP sing 98 n n C2' C3' DCP sing 99 n n C2' "H2'1" DCP sing 100 n n C2' "H2'2" DCP sing 101 n n C3' C4' DCP sing 102 n n C3' O3' DCP sing 103 n n C3' H3' DCP sing 104 n n C4' O4' DCP sing 105 n n C4' C5' DCP sing 106 n n C4' H4' DCP sing 107 n n O3' HO3' DCP sing 108 n n C5' O5' DCP sing 109 n n C5' "H5'1" DCP sing 110 n n C5' "H5'2" DCP sing 111 n n O5' PA DCP sing 112 n n PA O1A DCP doub 113 n n PA O2A DCP sing 114 n n PA O3A DCP sing 115 n n O2A HOA2 DCP sing 116 n n O3A PB DCP sing 117 n n PB O1B DCP doub 118 n n PB O2B DCP sing 119 n n PB O3B DCP sing 120 n n O2B HOB2 DCP sing 121 n n O3B PG DCP sing 122 n n PG O1G DCP doub 123 n n PG O2G DCP sing 124 n n PG O3G DCP sing 125 n n O2G HOG2 DCP sing 126 n n O3G HOG3 DCP sing 127 n n # _atom_sites.entry_id 1PEO _atom_sites.fract_transf_matrix[1][1] 0.010107 _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] 0.010107 _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] 0.003458 _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 MG A 1 715 701 MG MG . C 3 DCP A 1 716 700 DCP DCP . # 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 N1 DCP . . . C 3 -0.523 17.901 149.763 1 15.65 ? N1 DCP 716 A 1 HETATM 2 C C2 DCP . . . C 3 0.722 18.277 150.236 1 19.47 ? C2 DCP 716 A 1 HETATM 3 N N3 DCP . . . C 3 1.203 17.989 151.518 1 13.64 ? N3 DCP 716 A 1 HETATM 4 C C4 DCP . . . C 3 0.359 17.277 152.346 1 15.41 ? C4 DCP 716 A 1 HETATM 5 C C5 DCP . . . C 3 -0.905 16.88 151.947 1 9.33 ? C5 DCP 716 A 1 HETATM 6 C C6 DCP . . . C 3 -1.351 17.202 150.628 1 3.74 ? C6 DCP 716 A 1 HETATM 7 O O2 DCP . . . C 3 1.481 18.876 149.579 1 28.8 ? O2 DCP 716 A 1 HETATM 8 N N4 DCP . . . C 3 0.76 16.993 153.514 1 21.75 ? N4 DCP 716 A 1 HETATM 9 C C1' DCP . . . C 3 -1.036 18.232 148.442 1 15.35 ? C1' DCP 716 A 1 HETATM 10 C C2' DCP . . . C 3 -0.971 17.203 147.319 1 17.27 ? C2' DCP 716 A 1 HETATM 11 C C3' DCP . . . C 3 -2.248 17.305 146.48 1 20.55 ? C3' DCP 716 A 1 HETATM 12 C C4' DCP . . . C 3 -3.163 18.124 147.326 1 21.14 ? C4' DCP 716 A 1 HETATM 13 O O4' DCP . . . C 3 -2.41 18.585 148.455 1 18.06 ? O4' DCP 716 A 1 HETATM 14 O O3' DCP . . . C 3 -2.222 17.997 145.23 1 22.94 ? O3' DCP 716 A 1 HETATM 15 C C5' DCP . . . C 3 -4.292 17.215 147.742 1 22.89 ? C5' DCP 716 A 1 HETATM 16 O O5' DCP . . . C 3 -3.838 16.104 148.518 1 22.19 ? O5' DCP 716 A 1 HETATM 17 P PA DCP . . . C 3 -5.021 15.183 149.094 1 25.91 ? PA DCP 716 A 1 HETATM 18 O O1A DCP . . . C 3 -4.467 13.833 149.556 1 21.65 ? O1A DCP 716 A 1 HETATM 19 O O2A DCP . . . C 3 -6.33 15.278 148.326 1 24 ? O2A DCP 716 A 1 HETATM 20 O O3A DCP . . . C 3 -5.417 16.095 150.339 1 22.76 ? O3A DCP 716 A 1 HETATM 21 P PB DCP . . . C 3 -6.76 15.765 151.143 1 23.9 ? PB DCP 716 A 1 HETATM 22 O O1B DCP . . . C 3 -7.783 15.154 150.229 1 20.81 ? O1B DCP 716 A 1 HETATM 23 O O2B DCP . . . C 3 -6.416 15.251 152.518 1 25.31 ? O2B DCP 716 A 1 HETATM 24 O O3B DCP . . . C 3 -7.117 17.262 151.498 1 25.16 ? O3B DCP 716 A 1 HETATM 25 P PG DCP . . . C 3 -8.238 17.957 150.635 1 24.99 ? PG DCP 716 A 1 HETATM 26 O O1G DCP . . . C 3 -9.411 17.07 150.898 1 25.57 ? O1G DCP 716 A 1 HETATM 27 O O2G DCP . . . C 3 -7.984 19.22 151.354 1 30.33 ? O2G DCP 716 A 1 HETATM 28 O O3G DCP . . . C 3 -7.885 18.111 149.206 1 24.14 ? O3G DCP 716 A 1 # _model_server_stats.io_time_ms 55 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #