data_5DDY # _model_server_result.job_id 6RHKlKyHcuPWVMMdKfuyZw _model_server_result.datetime_utc '2024-11-28 02:07:29' _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 5ddy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":603}' # _entry.id 5DDY # _exptl.entry_id 5DDY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 467.157 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 4 _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 5DDY _cell.length_a 206.015 _cell.length_b 206.015 _cell.length_c 114.266 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5DDY _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 43 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 ? monomeric 1 author_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,F,G,H,U 1 1 B,I,J,K,L,V 2 1 C,M,N,O,P 3 1 D,Q,R,S,T 4 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 G N N ? 4 K N N ? 4 O N N ? 4 S 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 disulf ? disulf1 A SG CYS 303 A CYS 543 1_555 D SG CYS 303 G CYS 543 7_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 B SG CYS 303 C CYS 543 1_555 C SG CYS 303 E CYS 543 3_454 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc1 A O SER 99 A SER 339 1_555 H MN MN . A MN 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.68 ? metalc ? metalc2 A OD1 ASP 187 A ASP 427 1_555 E MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc3 A OD2 ASP 189 A ASP 429 1_555 E MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? metalc ? metalc4 A OD1 ASP 189 A ASP 429 1_555 F MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.517 ? metalc ? metalc5 A OD2 ASP 250 A ASP 490 1_555 F MN MN . A MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc6 E MG MG . A MG 601 1_555 G O2G DCP . A DCP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.779 ? metalc ? metalc7 E MG MG . A MG 601 1_555 G O2A DCP . A DCP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.592 ? metalc ? metalc8 E MG MG . A MG 601 1_555 G O2B DCP . A DCP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc9 B O ASP 187 C ASP 427 1_555 I MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.696 ? metalc ? metalc10 B OD1 ASP 187 C ASP 427 1_555 I MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? metalc ? metalc11 B OD2 ASP 187 C ASP 427 1_555 J MN MN . C MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc12 B OD1 ASP 189 C ASP 429 1_555 I MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc13 B OD2 ASP 189 C ASP 429 1_555 J MN MN . C MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? metalc ? metalc14 B OD2 ASP 250 C ASP 490 1_555 J MN MN . C MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc15 I MG MG . C MG 601 1_555 K O2B DCP . C DCP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.226 ? metalc ? metalc16 I MG MG . C MG 601 1_555 K O2A DCP . C DCP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.7 ? metalc ? metalc17 I MG MG . C MG 601 1_555 K O2G DCP . C DCP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc18 J MN MN . C MN 602 1_555 K O2A DCP . C DCP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.665 ? metalc ? metalc19 C OD1 ASP 187 E ASP 427 1_555 M MG MG . E MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? metalc ? metalc20 C OD2 ASP 187 E ASP 427 1_555 N MN MN . E MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.623 ? metalc ? metalc21 C OD2 ASP 189 E ASP 429 1_555 M MG MG . E MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc22 C OD1 ASP 189 E ASP 429 1_555 N MN MN . E MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? metalc ? metalc23 C OD2 ASP 250 E ASP 490 1_555 N MN MN . E MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc24 M MG MG . E MG 601 1_555 O O2B DCP . E DCP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc25 M MG MG . E MG 601 1_555 O O2A DCP . E DCP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.642 ? metalc ? metalc26 M MG MG . E MG 601 1_555 O O2G DCP . E DCP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? metalc ? metalc27 D O ASP 187 G ASP 427 1_555 Q MG MG . G MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.722 ? metalc ? metalc28 D OD1 ASP 187 G ASP 427 1_555 Q MG MG . G MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? metalc ? metalc29 D OD2 ASP 189 G ASP 429 1_555 Q MG MG . G MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.619 ? metalc ? metalc30 D OD2 ASP 250 G ASP 490 1_555 R MN MN . G MN 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc31 Q MG MG . G MG 601 1_555 S O2B DCP . G DCP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? metalc ? metalc32 Q MG MG . G MG 601 1_555 S O2G DCP . G DCP 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.4 ? # _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 5DDY _atom_sites.fract_transf_matrix[1][1] 0.004854 _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] 0.004854 _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] 0.008752 _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 E 2 MG A 1 601 601 MG MG . F 3 MN A 1 602 602 MN MN . G 4 DCP A 1 603 603 DCP DCP . H 3 MN A 1 604 604 MN MN . I 2 MG C 1 601 601 MG MG . J 3 MN C 1 602 602 MN MN . K 4 DCP C 1 603 603 DCP DCP . L 3 MN C 1 604 604 MN MN . M 2 MG E 1 601 601 MG MG . N 3 MN E 1 602 602 MN MN . O 4 DCP E 1 603 603 DCP DCP . P 3 MN E 1 604 604 MN MN . Q 2 MG G 1 601 601 MG MG . R 3 MN G 1 602 602 MN MN . S 4 DCP G 1 603 603 DCP DCP . T 3 MN G 1 604 604 MN MN . U 5 HOH A 1 701 701 HOH HOH . U 5 HOH A 2 702 702 HOH HOH . V 5 HOH C 1 701 701 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 N1 DCP . . . G 4 -42.151 -18.26 3.88 1 112.4 ? N1 DCP 603 A 1 HETATM 2 C C2 DCP . . . G 4 -41.587 -19.533 4.164 1 114.31 ? C2 DCP 603 A 1 HETATM 3 N N3 DCP . . . G 4 -41.545 -20.518 3.092 1 122.32 ? N3 DCP 603 A 1 HETATM 4 C C4 DCP . . . G 4 -42.026 -20.199 1.895 1 122.78 ? C4 DCP 603 A 1 HETATM 5 C C5 DCP . . . G 4 -42.624 -18.814 1.627 1 113.35 ? C5 DCP 603 A 1 HETATM 6 C C6 DCP . . . G 4 -42.667 -17.896 2.623 1 109.06 ? C6 DCP 603 A 1 HETATM 7 O O2 DCP . . . G 4 -41.144 -19.821 5.269 1 110.5 ? O2 DCP 603 A 1 HETATM 8 N N4 DCP . . . G 4 -41.984 -21.165 0.832 1 117.87 ? N4 DCP 603 A 1 HETATM 9 C C1' DCP . . . G 4 -42.197 -17.251 4.945 1 106.09 ? C1' DCP 603 A 1 HETATM 10 C C2' DCP . . . G 4 -40.952 -16.42 5.035 1 108.52 ? C2' DCP 603 A 1 HETATM 11 C C3' DCP . . . G 4 -41.357 -15.163 4.34 1 105.89 ? C3' DCP 603 A 1 HETATM 12 C C4' DCP . . . G 4 -42.785 -15.06 4.733 1 104.56 ? C4' DCP 603 A 1 HETATM 13 O O4' DCP . . . G 4 -43.28 -16.351 4.839 1 111.25 ? O4' DCP 603 A 1 HETATM 14 O O3' DCP . . . G 4 -40.583 -14.06 4.691 1 119.39 ? O3' DCP 603 A 1 HETATM 15 C C5' DCP . . . G 4 -43.64 -14.168 3.841 1 113.05 ? C5' DCP 603 A 1 HETATM 16 O O5' DCP . . . G 4 -43.75 -14.686 2.557 1 109.54 ? O5' DCP 603 A 1 HETATM 17 P PA DCP . . . G 4 -43.351 -13.802 1.298 1 117.21 ? PA DCP 603 A 1 HETATM 18 O O1A DCP . . . G 4 -43.789 -14.552 0.054 1 108.12 ? O1A DCP 603 A 1 HETATM 19 O O2A DCP . . . G 4 -44.103 -12.493 1.385 1 126.24 ? O2A DCP 603 A 1 HETATM 20 O O3A DCP . . . G 4 -41.782 -13.566 1.294 1 111.06 ? O3A DCP 603 A 1 HETATM 21 P PB DCP . . . G 4 -41.097 -12.145 1.471 1 97.14 ? PB DCP 603 A 1 HETATM 22 O O1B DCP . . . G 4 -39.929 -12.269 2.425 1 109.76 ? O1B DCP 603 A 1 HETATM 23 O O2B DCP . . . G 4 -42.055 -11.158 2.098 1 101.24 ? O2B DCP 603 A 1 HETATM 24 O O3B DCP . . . G 4 -40.586 -11.619 0.068 1 96.04 ? O3B DCP 603 A 1 HETATM 25 P PG DCP . . . G 4 -41.457 -10.655 -0.835 1 106.17 ? PG DCP 603 A 1 HETATM 26 O O1G DCP . . . G 4 -41.479 -11.078 -2.287 1 105.41 ? O1G DCP 603 A 1 HETATM 27 O O2G DCP . . . G 4 -42.863 -10.61 -0.289 1 111.53 ? O2G DCP 603 A 1 HETATM 28 O O3G DCP . . . G 4 -40.86 -9.264 -0.83 1 114.64 ? O3G DCP 603 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 556 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 28 #