data_5W0U # _model_server_result.job_id JwDp6Tu39YBSzo8oqp8yMg _model_server_result.datetime_utc '2024-11-22 11:40:17' _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 5w0u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":2002}' # _entry.id 5W0U # _exptl.entry_id 5W0U _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 307.197 _entity.id 5 _entity.src_method man _entity.type non-polymer _entity.pdbx_description "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90.14 _cell.angle_gamma 90 _cell.entry_id 5W0U _cell.length_a 125.005 _cell.length_b 39.777 _cell.length_c 153.935 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5W0U _symmetry.cell_setting ? _symmetry.Int_Tables_number 3 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? trimeric 3 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,E,F,G,H,L 1 1 D,I,J,K,M 2 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 ? 5 F N N ? 5 J 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 metalc ? metalc1 A O ASN 368 B ASN 368 1_555 G CA CA . B CA 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.119 ? metalc ? metalc2 A OD1 ASP 413 B ASP 1045 1_555 G CA CA . B CA 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.966 ? metalc ? metalc3 A ND1 HIS 424 B HIS 1056 1_555 E ZN ZN . B ZN 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc4 A SG CYS 455 B CYS 1087 1_555 E ZN ZN . B ZN 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc5 A SG CYS 458 B CYS 1090 1_555 E ZN ZN . B ZN 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc6 E ZN ZN . B ZN 2001 1_555 L O HOH . B HOH 4001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.781 ? metalc ? metalc7 D O THR 367 A THR 367 1_555 K CA CA . A CA 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.065 ? metalc ? metalc8 D O ASN 368 A ASN 368 1_555 K CA CA . A CA 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.003 ? metalc ? metalc9 D O ALA 370 A ALA 370 1_555 K CA CA . A CA 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.929 ? metalc ? metalc10 D OD1 ASP 413 A ASP 1045 1_555 K CA CA . A CA 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.855 ? metalc ? metalc11 D ND1 HIS 424 A HIS 1056 1_555 I ZN ZN . A ZN 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc12 D SG CYS 455 A CYS 1087 1_555 I ZN ZN . A ZN 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc13 D SG CYS 458 A CYS 1090 1_555 I ZN ZN . A ZN 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc14 I ZN ZN . A ZN 2001 1_555 M O HOH . A HOH 4001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? hydrog WATSON-CRICK hydrog1 B N1 DG 1 D DG 1 1_555 C N3 DC 12 G DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B N2 DG 1 D DG 1 1_555 C O2 DC 12 G DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B O6 DG 1 D DG 1 1_555 C N4 DC 12 G DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N3 DT 2 D DT 2 1_555 C N1 DA 11 G DA 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O4 DT 2 D DT 2 1_555 C N6 DA 11 G DA 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N3 DT 3 D DT 3 1_555 C N1 DA 10 G DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B O4 DT 3 D DT 3 1_555 C N6 DA 10 G DA 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N3 DC 4 D DC 4 1_555 C N1 DG 9 G DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N4 DC 4 D DC 4 1_555 C O6 DG 9 G DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B O2 DC 4 D DC 4 1_555 C N2 DG 9 G DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N1 DA 5 D DA 5 1_555 C N3 DT 8 G DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N6 DA 5 D DA 5 1_555 C O4 DT 8 G DT 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B N1 DA 6 D DA 6 1_555 C N3 DT 7 G DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N6 DA 6 D DA 6 1_555 C O4 DT 7 G DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N1 DG 7 D DG 7 1_555 C N3 DC 6 G DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B N2 DG 7 D DG 7 1_555 C O2 DC 6 G DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B O6 DG 7 D DG 7 1_555 C N4 DC 6 G DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B N1 DG 8 D DG 8 1_555 C N3 DC 5 G DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 B N2 DG 8 D DG 8 1_555 C O2 DC 5 G DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 B O6 DG 8 D DG 8 1_555 C N4 DC 5 G DC 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 B N3 DC 9 D DC 9 1_555 C N1 DG 4 G DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 B N4 DC 9 D DC 9 1_555 C O6 DG 4 G DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 B O2 DC 9 D DC 9 1_555 C N2 DG 4 G DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 B N3 DC 10 D DC 10 1_555 C N1 DG 3 G DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 B N4 DC 10 D DC 10 1_555 C O6 DG 3 G DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 B O2 DC 10 D DC 10 1_555 C N2 DG 3 G DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 B N1 DA 11 D DA 11 1_555 C N3 DT 2 G DT 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 B N6 DA 11 D DA 11 1_555 C O4 DT 2 G DT 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 B N1 DG 12 D DG 12 1_555 C N3 DC 1 G DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 B N2 DG 12 D DG 12 1_555 C O2 DC 1 G DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 B O6 DG 12 D DG 12 1_555 C N4 DC 1 G DC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C9 H14 N3 O7 P' _chem_comp.formula_weight 307.197 _chem_comp.id DCM _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" _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 DCM sing 156 n n N1 C6 DCM sing 157 n n N1 C1' DCM sing 158 n n C2 N3 DCM sing 159 n n C2 O2 DCM doub 160 n n N3 C4 DCM doub 161 n n C4 C5 DCM sing 162 n n C4 N4 DCM sing 163 n n C5 C6 DCM doub 164 n n C5 H5 DCM sing 165 n n C6 H6 DCM sing 166 n n N4 HN41 DCM sing 167 n n N4 HN42 DCM sing 168 n n C1' C2' DCM sing 169 n n C1' O4' DCM sing 170 n n C1' H1' DCM sing 171 n n C2' C3' DCM sing 172 n n C2' "H2'1" DCM sing 173 n n C2' "H2'2" DCM sing 174 n n C3' C4' DCM sing 175 n n C3' O3' DCM sing 176 n n C3' H3' DCM sing 177 n n C4' O4' DCM sing 178 n n C4' C5' DCM sing 179 n n C4' H4' DCM sing 180 n n O3' HO3' DCM sing 181 n n C5' O5' DCM sing 182 n n C5' "H5'1" DCM sing 183 n n C5' "H5'2" DCM sing 184 n n O5' P DCM sing 185 n n P O1P DCM doub 186 n n P O2P DCM sing 187 n n P O3P DCM sing 188 n n O2P HOP2 DCM sing 189 n n O3P HOP3 DCM sing 190 n n # _atom_sites.entry_id 5W0U _atom_sites.fract_transf_matrix[1][1] 0.008 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00002 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.02514 _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] 0.006496 _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 4 ZN B 1 2001 2001 ZN ZN . F 5 DCM B 1 2002 3001 DCM DCM . G 6 CA B 1 2003 5001 CA CA . H 7 GOL B 1 2004 1 GOL GOL . I 4 ZN A 1 2001 2001 ZN ZN . J 5 DCM A 1 2002 3001 DCM DCM . K 6 CA A 1 2003 5001 CA CA . L 8 HOH B 1 4001 4001 HOH HOH . M 8 HOH A 1 4001 4001 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 DCM . . . J 5 318.248 24.09 1264.905 1 105.99 ? N1 DCM 2002 A 1 HETATM 2 C C2 DCM . . . J 5 316.941 23.934 1265.414 1 104.6 ? C2 DCM 2002 A 1 HETATM 3 N N3 DCM . . . J 5 316.122 25.002 1265.533 1 93.01 ? N3 DCM 2002 A 1 HETATM 4 C C4 DCM . . . J 5 316.544 26.231 1265.167 1 92.27 ? C4 DCM 2002 A 1 HETATM 5 C C5 DCM . . . J 5 317.828 26.403 1264.665 1 100.51 ? C5 DCM 2002 A 1 HETATM 6 C C6 DCM . . . J 5 318.673 25.307 1264.542 1 103.53 ? C6 DCM 2002 A 1 HETATM 7 O O2 DCM . . . J 5 316.536 22.802 1265.756 1 106.28 ? O2 DCM 2002 A 1 HETATM 8 N N4 DCM . . . J 5 315.716 27.296 1265.29 1 112.79 ? N4 DCM 2002 A 1 HETATM 9 C C1' DCM . . . J 5 319.121 22.914 1264.785 1 111.47 ? C1' DCM 2002 A 1 HETATM 10 C C2' DCM . . . J 5 318.382 21.803 1264.05 1 114.77 ? C2' DCM 2002 A 1 HETATM 11 C C3' DCM . . . J 5 319.222 21.473 1262.831 1 121.85 ? C3' DCM 2002 A 1 HETATM 12 C C4' DCM . . . J 5 320.427 22.398 1262.875 1 134.1 ? C4' DCM 2002 A 1 HETATM 13 O O4' DCM . . . J 5 320.309 23.214 1264.043 1 120.35 ? O4' DCM 2002 A 1 HETATM 14 O O3' DCM . . . J 5 319.649 20.109 1262.884 1 132.14 ? O3' DCM 2002 A 1 HETATM 15 C C5' DCM . . . J 5 320.492 23.281 1261.635 1 135.45 ? C5' DCM 2002 A 1 HETATM 16 O O5' DCM . . . J 5 321.65 22.947 1260.874 1 147.54 ? O5' DCM 2002 A 1 HETATM 17 P P DCM . . . J 5 321.51 22.168 1259.472 1 181.86 ? P DCM 2002 A 1 HETATM 18 O O1P DCM . . . J 5 321.078 23.24 1258.501 1 189.84 ? O1P DCM 2002 A 1 HETATM 19 O O2P DCM . . . J 5 322.894 21.62 1259.22 1 163.24 ? O2P DCM 2002 A 1 HETATM 20 O O3P DCM . . . J 5 320.462 21.115 1259.744 1 164.2 ? O3P DCM 2002 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #