data_5XPD # _model_server_result.job_id dAYl6lZIJQYAVpRtycEU0g _model_server_result.datetime_utc '2025-07-03 23:03:00' _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 5xpd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 5XPD # _exptl.entry_id 5XPD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 307.197 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYCYTIDINE-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 93.85 _cell.angle_gamma 90 _cell.entry_id 5XPD _cell.length_a 75.78 _cell.length_b 42.831 _cell.length_c 116.553 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XPD _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _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 83 n n N1 C6 DCM sing 84 n n N1 C1' DCM sing 85 n n C2 N3 DCM sing 86 n n C2 O2 DCM doub 87 n n N3 C4 DCM doub 88 n n C4 C5 DCM sing 89 n n C4 N4 DCM sing 90 n n C5 C6 DCM doub 91 n n C5 H5 DCM sing 92 n n C6 H6 DCM sing 93 n n N4 HN41 DCM sing 94 n n N4 HN42 DCM sing 95 n n C1' C2' DCM sing 96 n n C1' O4' DCM sing 97 n n C1' H1' DCM sing 98 n n C2' C3' DCM sing 99 n n C2' "H2'1" DCM sing 100 n n C2' "H2'2" DCM sing 101 n n C3' C4' DCM sing 102 n n C3' O3' DCM sing 103 n n C3' H3' DCM sing 104 n n C4' O4' DCM sing 105 n n C4' C5' DCM sing 106 n n C4' H4' DCM sing 107 n n O3' HO3' DCM sing 108 n n C5' O5' DCM sing 109 n n C5' "H5'1" DCM sing 110 n n C5' "H5'2" DCM sing 111 n n O5' P DCM sing 112 n n P O1P DCM doub 113 n n P O2P DCM sing 114 n n P O3P DCM sing 115 n n O2P HOP2 DCM sing 116 n n O3P HOP3 DCM sing 117 n n # _atom_sites.entry_id 5XPD _atom_sites.fract_transf_matrix[1][1] 0.013196 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000889 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.023348 _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] 0.008599 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id DCM _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 301 _pdbx_nonpoly_scheme.auth_seq_num 1 _pdbx_nonpoly_scheme.pdb_mon_id DCM _pdbx_nonpoly_scheme.auth_mon_id DCM _pdbx_nonpoly_scheme.pdb_ins_code . # 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 . . . B 2 -12.287 0.238 39.661 1 60.76 ? N1 DCM 301 A 1 HETATM 2 C C2 DCM . . . B 2 -12.272 0.93 40.913 1 54.53 ? C2 DCM 301 A 1 HETATM 3 N N3 DCM . . . B 2 -11.454 2.112 41.027 1 59.59 ? N3 DCM 301 A 1 HETATM 4 C C4 DCM . . . B 2 -10.766 2.514 40.02 1 62.53 ? C4 DCM 301 A 1 HETATM 5 C C5 DCM . . . B 2 -10.798 1.747 38.677 1 60.59 ? C5 DCM 301 A 1 HETATM 6 C C6 DCM . . . B 2 -11.534 0.669 38.549 1 64.48 ? C6 DCM 301 A 1 HETATM 7 O O2 DCM . . . B 2 -13.027 0.482 42.012 1 46.26 ? O2 DCM 301 A 1 HETATM 8 N N4 DCM . . . B 2 -9.948 3.7 40.127 1 45.91 ? N4 DCM 301 A 1 HETATM 9 C C1' DCM . . . B 2 -13.072 -0.919 39.473 1 57.67 ? C1' DCM 301 A 1 HETATM 10 C C2' DCM . . . B 2 -14.531 -0.529 39.581 1 51.21 ? C2' DCM 301 A 1 HETATM 11 C C3' DCM . . . B 2 -15.192 -1.172 38.421 1 46.85 ? C3' DCM 301 A 1 HETATM 12 C C4' DCM . . . B 2 -14.111 -1.567 37.47 1 51.19 ? C4' DCM 301 A 1 HETATM 13 O O4' DCM . . . B 2 -12.853 -1.365 38.118 1 52.39 ? O4' DCM 301 A 1 HETATM 14 O O3' DCM . . . B 2 -15.925 -2.308 38.879 1 42.94 ? O3' DCM 301 A 1 HETATM 15 C C5' DCM . . . B 2 -14.248 -0.704 36.233 1 43.48 ? C5' DCM 301 A 1 HETATM 16 O O5' DCM . . . B 2 -14.89 -1.492 35.278 1 46.13 ? O5' DCM 301 A 1 HETATM 17 P P DCM . . . B 2 -15.331 -0.832 33.846 1 78.84 ? P DCM 301 A 1 HETATM 18 O O1P DCM . . . B 2 -14.889 -1.614 32.699 1 46.55 ? O1P DCM 301 A 1 HETATM 19 O O2P DCM . . . B 2 -16.778 -0.76 33.703 1 42.92 ? O2P DCM 301 A 1 HETATM 20 O O3P DCM . . . B 2 -14.863 0.524 33.573 1 61.67 ? O3P DCM 301 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 20 #