data_5C53 # _model_server_result.job_id IIcxuYs57PtRnY7FYBss4A _model_server_result.datetime_utc '2024-10-19 03:57:16' _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 5c53 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":101}' # _entry.id 5C53 # _exptl.entry_id 5C53 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 291.198 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE" _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 5C53 _cell.length_a 217.447 _cell.length_b 217.447 _cell.length_c 163.593 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5C53 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 41 21 2' # _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 _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 7 _struct_asym.id I _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 covale ? covale1 E O3' DA 21 P DA 23 1_555 I P DOC . P DOC 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.606 ? metalc ? metalc1 A OD1 ASP 856 A ASP 890 1_555 G MG MG . A MG 4002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.664 ? metalc ? metalc2 A O VAL 857 A VAL 891 1_555 G MG MG . A MG 4002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? metalc ? metalc3 A OD2 ASP 1101 A ASP 1135 1_555 F MG MG . A MG 4001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.998 ? metalc ? metalc4 A OD2 ASP 1101 A ASP 1135 1_555 G MG MG . A MG 4002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc5 F MG MG . A MG 4001 1_555 H O2A 4Y3 . A 4Y3 4003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? metalc ? metalc6 F MG MG . A MG 4001 1_555 H O5' 4Y3 . A 4Y3 4003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.843 ? metalc ? metalc7 G MG MG . A MG 4002 1_555 H O1G 4Y3 . A 4Y3 4003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.778 ? metalc ? metalc8 G MG MG . A MG 4002 1_555 H O2A 4Y3 . A 4Y3 4003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.489 ? metalc ? metalc9 G MG MG . A MG 4002 1_555 H O3B 4Y3 . A 4Y3 4003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.559 ? metalc ? metalc10 G MG MG . A MG 4002 1_555 H O2B 4Y3 . A 4Y3 4003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.602 ? hydrog WATSON-CRICK hydrog1 D N3 DT 6 T DT 6 1_555 E N1 DA 21 P DA 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 D O4 DT 6 T DT 6 1_555 E N6 DA 21 P DA 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 D N1 DA 7 T DA 7 1_555 E N3 DT 20 P DT 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 D N6 DA 7 T DA 7 1_555 E O4 DT 20 P DT 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog5 D O2 DC 8 T DC 8 1_555 E N2 DG 19 P DG 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 D N1 DG 9 T DG 9 1_555 E N3 DC 18 P DC 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 D N2 DG 9 T DG 9 1_555 E O2 DC 18 P DC 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 D O6 DG 9 T DG 9 1_555 E N4 DC 18 P DC 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 D N1 DG 10 T DG 10 1_555 E N3 DC 17 P DC 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 D N2 DG 10 T DG 10 1_555 E O2 DC 17 P DC 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 D O6 DG 10 T DG 10 1_555 E N4 DC 17 P DC 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 D N3 DC 11 T DC 11 1_555 E N1 DG 16 P DG 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 D N4 DC 11 T DC 11 1_555 E O6 DG 16 P DG 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 D O2 DC 11 T DC 11 1_555 E N2 DG 16 P DG 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 D N1 DA 12 T DA 12 1_555 E N3 DT 15 P DT 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 D N6 DA 12 T DA 12 1_555 E O4 DT 15 P DT 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 D N3 DC 13 T DC 13 1_555 E N1 DG 14 P DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 D N4 DC 13 T DC 13 1_555 E O6 DG 14 P DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 D O2 DC 13 T DC 13 1_555 E N2 DG 14 P DG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 D N3 DT 14 T DT 14 1_555 E N1 DA 13 P DA 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 D O4 DT 14 T DT 14 1_555 E N6 DA 13 P DA 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog22 D N2 DG 15 T DG 15 1_555 E O2 DC 12 P DC 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 D N1 DG 16 T DG 16 1_555 E N3 DC 11 P DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 D N2 DG 16 T DG 16 1_555 E O2 DC 11 P DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 D O6 DG 16 T DG 16 1_555 E N4 DC 11 P DC 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 D N3 DC 17 T DC 17 1_555 E N1 DG 10 P DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 D N4 DC 17 T DC 17 1_555 E O6 DG 10 P DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 D O2 DC 17 T DC 17 1_555 E N2 DG 10 P DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DC-DG PAIR' hydrog29 D N4 DC 18 T DC 18 1_555 E O6 DG 8 P DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 D N3 DC 18 T DC 18 1_555 E N1 DG 9 P DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 D N4 DC 18 T DC 18 1_555 E O6 DG 9 P DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 D O2 DC 18 T DC 18 1_555 E N2 DG 9 P DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 D N3 DC 19 T DC 19 1_555 E N1 DG 8 P DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 D N4 DC 19 T DC 19 1_555 E O6 DG 8 P DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 D O2 DC 19 T DC 19 1_555 E N2 DG 8 P DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 D N3 DT 20 T DT 20 1_555 E N1 DA 7 P DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 D O4 DT 20 T DT 20 1_555 E N6 DA 7 P DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 D N3 DC 21 T DC 21 1_555 E N1 DG 6 P DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog39 D N4 DC 21 T DC 21 1_555 E O6 DG 6 P DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog40 D O2 DC 21 T DC 21 1_555 E N2 DG 6 P DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog41 D N1 DG 22 T DG 22 1_555 E N3 DC 5 P DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog42 D N2 DG 22 T DG 22 1_555 E O2 DC 5 P DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog43 D O6 DG 22 T DG 22 1_555 E N4 DC 5 P DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog44 D N3 DT 23 T DT 23 1_555 E N1 DA 4 P DA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog45 D O4 DT 23 T DT 23 1_555 E N6 DA 4 P DA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C9 H14 N3 O6 P' _chem_comp.formula_weight 291.198 _chem_comp.id DOC _chem_comp.mon_nstd_flag n _chem_comp.name "2',3'-DIDEOXYCYTIDINE-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 N1 C2 DOC sing 239 n n N1 C6 DOC sing 240 n n N1 C1' DOC sing 241 n n C2 N3 DOC sing 242 n n C2 O2 DOC doub 243 n n N3 C4 DOC doub 244 n n C4 C5 DOC sing 245 n n C4 N4 DOC sing 246 n n C5 C6 DOC doub 247 n n C5 H5 DOC sing 248 n n C6 H6 DOC sing 249 n n N4 HN41 DOC sing 250 n n N4 HN42 DOC sing 251 n n C1' C2' DOC sing 252 n n C1' O4' DOC sing 253 n n C1' H1' DOC sing 254 n n C2' C3' DOC sing 255 n n C2' H2' DOC sing 256 n n C2' "H2''" DOC sing 257 n n C3' C4' DOC sing 258 n n C3' "H3'1" DOC sing 259 n n C3' "H3'2" DOC sing 260 n n C4' O4' DOC sing 261 n n C4' C5' DOC sing 262 n n C4' H4' DOC sing 263 n n C5' O5' DOC sing 264 n n C5' H5' DOC sing 265 n n C5' "H5''" DOC sing 266 n n O5' P DOC sing 267 n n P OP1 DOC doub 268 n n P OP2 DOC sing 269 n n P OP3 DOC sing 270 n n OP2 HOP2 DOC sing 271 n n OP3 HOP3 DOC sing 272 n n # _atom_sites.entry_id 5C53 _atom_sites.fract_transf_matrix[1][1] 0.004599 _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] 0.004599 _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] 0.006113 _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 5 MG A 1 4001 4001 MG MG . G 5 MG A 1 4002 4002 MG MG . H 6 4Y3 A 1 4003 10 4Y3 PFT . I 7 DOC P 1 101 24 DOC 2DC . # 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 DOC . . . I 7 22.695 54.03 -30.536 1 98.94 ? N1 DOC 101 P 1 HETATM 2 C C2 DOC . . . I 7 23.499 52.911 -30.291 1 95.04 ? C2 DOC 101 P 1 HETATM 3 N N3 DOC . . . I 7 22.917 51.687 -30.22 1 94.63 ? N3 DOC 101 P 1 HETATM 4 C C4 DOC . . . I 7 21.599 51.565 -30.382 1 97.92 ? C4 DOC 101 P 1 HETATM 5 C C5 DOC . . . I 7 20.764 52.693 -30.632 1 97.24 ? C5 DOC 101 P 1 HETATM 6 C C6 DOC . . . I 7 21.348 53.894 -30.7 1 97.8 ? C6 DOC 101 P 1 HETATM 7 O O2 DOC . . . I 7 24.719 53.065 -30.145 1 98.02 ? O2 DOC 101 P 1 HETATM 8 N N4 DOC . . . I 7 21.071 50.34 -30.304 1 99.38 ? N4 DOC 101 P 1 HETATM 9 C C1' DOC . . . I 7 23.319 55.381 -30.616 1 91.76 ? C1' DOC 101 P 1 HETATM 10 C C2' DOC . . . I 7 23.796 55.754 -32.025 1 94.03 ? C2' DOC 101 P 1 HETATM 11 C C3' DOC . . . I 7 22.698 56.698 -32.509 1 97.42 ? C3' DOC 101 P 1 HETATM 12 C C4' DOC . . . I 7 22.286 57.386 -31.224 1 96.28 ? C4' DOC 101 P 1 HETATM 13 O O4' DOC . . . I 7 22.363 56.35 -30.221 1 94.01 ? O4' DOC 101 P 1 HETATM 14 C C5' DOC . . . I 7 20.891 57.985 -31.234 1 92.67 ? C5' DOC 101 P 1 HETATM 15 O O5' DOC . . . I 7 19.931 57.028 -31.664 1 94.4 ? O5' DOC 101 P 1 HETATM 16 P P DOC . . . I 7 18.37 57.351 -31.542 1 94.15 ? P DOC 101 P 1 HETATM 17 O OP1 DOC . . . I 7 18.105 58.671 -32.156 1 91.72 ? OP1 DOC 101 P 1 HETATM 18 O OP2 DOC . . . I 7 17.627 56.16 -32.008 1 92.2 ? OP2 DOC 101 P 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 292 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 18 #