data_2YK6 # _model_server_result.job_id zLGlz_7HtRa8_A-hI9ooQQ _model_server_result.datetime_utc '2024-10-27 14:24:45' _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 2yk6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1374}' # _entry.id 2YK6 # _exptl.entry_id 2YK6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 403.176 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "CYTIDINE-5'-DIPHOSPHATE" _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 2YK6 _cell.length_a 86.099 _cell.length_b 123.51 _cell.length_c 41.652 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2YK6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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' 2_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 86.099 123.51 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 H15 N3 O11 P2' _chem_comp.formula_weight 403.176 _chem_comp.id CDP _chem_comp.mon_nstd_flag . _chem_comp.name "CYTIDINE-5'-DIPHOSPHATE" _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 O3B PB CDP sing 107 n n PB O1B CDP doub 108 n n PB O2B CDP sing 109 n n PB O3A CDP sing 110 n n O3A PA CDP sing 111 n n PA O1A CDP doub 112 n n PA O2A CDP sing 113 n n PA O5' CDP sing 114 n n O5' C5' CDP sing 115 n n C5' C4' CDP sing 116 n n C5' "H5'1" CDP sing 117 n n C5' "H5'2" CDP sing 118 n n C4' O4' CDP sing 119 n n C4' C3' CDP sing 120 n n C4' H4' CDP sing 121 n n O4' C1' CDP sing 122 n n C3' O3' CDP sing 123 n n C3' C2' CDP sing 124 n n C3' H3' CDP sing 125 n n O3' HA CDP sing 126 n n C2' O2' CDP sing 127 n n C2' C1' CDP sing 128 n n C2' H2' CDP sing 129 n n O2' HB CDP sing 130 n n C1' N1 CDP sing 131 n n C1' H1' CDP sing 132 n n N1 C2 CDP sing 133 n n N1 C6 CDP sing 134 n n C2 O2 CDP doub 135 n n C2 N3 CDP sing 136 n n N3 C4 CDP doub 137 n n C4 N4 CDP sing 138 n n C4 C5 CDP sing 139 n n N4 H4N1 CDP sing 140 n n N4 H4N2 CDP sing 141 n n C5 C6 CDP doub 142 n n C5 H5 CDP sing 143 n n C6 H6 CDP sing 144 n n HO1 O2A CDP sing 145 n n HO2 O2B CDP sing 146 n n HO3 O3B CDP sing 147 n n # _atom_sites.entry_id 2YK6 _atom_sites.fract_transf_matrix[1][1] 0.011615 _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] 0.008097 _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] 0.024008 _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 CDP A 1 1374 1374 CDP CDP . C 3 1PE A 1 1375 1375 1PE 1PE . D 4 SO4 A 1 1376 1376 SO4 SO4 . E 5 HOH A 1 2001 2001 HOH HOH . E 5 HOH A 2 2002 2002 HOH HOH . E 5 HOH A 3 2003 2003 HOH HOH . E 5 HOH A 4 2004 2004 HOH HOH . E 5 HOH A 5 2005 2005 HOH HOH . E 5 HOH A 6 2006 2006 HOH HOH . E 5 HOH A 7 2007 2007 HOH HOH . E 5 HOH A 8 2008 2008 HOH HOH . E 5 HOH A 9 2009 2009 HOH HOH . E 5 HOH A 10 2010 2010 HOH HOH . E 5 HOH A 11 2011 2011 HOH HOH . E 5 HOH A 12 2012 2012 HOH HOH . E 5 HOH A 13 2013 2013 HOH HOH . E 5 HOH A 14 2014 2014 HOH HOH . E 5 HOH A 15 2015 2015 HOH HOH . E 5 HOH A 16 2016 2016 HOH HOH . E 5 HOH A 17 2017 2017 HOH HOH . E 5 HOH A 18 2018 2018 HOH HOH . E 5 HOH A 19 2019 2019 HOH HOH . E 5 HOH A 20 2020 2020 HOH HOH . E 5 HOH A 21 2021 2021 HOH HOH . E 5 HOH A 22 2022 2022 HOH HOH . E 5 HOH A 23 2023 2023 HOH HOH . E 5 HOH A 24 2024 2024 HOH HOH . E 5 HOH A 25 2025 2025 HOH HOH . E 5 HOH A 26 2026 2026 HOH HOH . E 5 HOH A 27 2027 2027 HOH HOH . E 5 HOH A 28 2028 2028 HOH HOH . E 5 HOH A 29 2029 2029 HOH HOH . E 5 HOH A 30 2030 2030 HOH HOH . E 5 HOH A 31 2031 2031 HOH HOH . E 5 HOH A 32 2032 2032 HOH HOH . E 5 HOH A 33 2033 2033 HOH HOH . E 5 HOH A 34 2034 2034 HOH HOH . E 5 HOH A 35 2035 2035 HOH HOH . E 5 HOH A 36 2036 2036 HOH HOH . E 5 HOH A 37 2037 2037 HOH HOH . E 5 HOH A 38 2038 2038 HOH HOH . E 5 HOH A 39 2039 2039 HOH HOH . E 5 HOH A 40 2040 2040 HOH HOH . E 5 HOH A 41 2041 2041 HOH HOH . E 5 HOH A 42 2042 2042 HOH HOH . E 5 HOH A 43 2043 2043 HOH HOH . E 5 HOH A 44 2044 2044 HOH HOH . E 5 HOH A 45 2045 2045 HOH HOH . E 5 HOH A 46 2046 2046 HOH HOH . E 5 HOH A 47 2047 2047 HOH HOH . E 5 HOH A 48 2048 2048 HOH HOH . E 5 HOH A 49 2049 2049 HOH HOH . E 5 HOH A 50 2050 2050 HOH HOH . E 5 HOH A 51 2051 2051 HOH HOH . E 5 HOH A 52 2052 2052 HOH HOH . E 5 HOH A 53 2053 2053 HOH HOH . E 5 HOH A 54 2054 2054 HOH HOH . E 5 HOH A 55 2055 2055 HOH HOH . E 5 HOH A 56 2056 2056 HOH HOH . E 5 HOH A 57 2057 2057 HOH HOH . E 5 HOH A 58 2058 2058 HOH HOH . E 5 HOH A 59 2059 2059 HOH HOH . E 5 HOH A 60 2060 2060 HOH HOH . E 5 HOH A 61 2061 2061 HOH HOH . E 5 HOH A 62 2062 2062 HOH HOH . E 5 HOH A 63 2063 2063 HOH HOH . E 5 HOH A 64 2064 2064 HOH HOH . E 5 HOH A 65 2065 2065 HOH HOH . E 5 HOH A 66 2066 2066 HOH HOH . E 5 HOH A 67 2067 2067 HOH HOH . E 5 HOH A 68 2068 2068 HOH HOH . E 5 HOH A 69 2069 2069 HOH HOH . E 5 HOH A 70 2070 2070 HOH HOH . E 5 HOH A 71 2071 2071 HOH HOH . E 5 HOH A 72 2072 2072 HOH HOH . E 5 HOH A 73 2073 2073 HOH HOH . E 5 HOH A 74 2074 2074 HOH HOH . E 5 HOH A 75 2075 2075 HOH HOH . E 5 HOH A 76 2076 2076 HOH HOH . E 5 HOH A 77 2077 2077 HOH HOH . E 5 HOH A 78 2078 2078 HOH HOH . E 5 HOH A 79 2079 2079 HOH HOH . E 5 HOH A 80 2080 2080 HOH HOH . E 5 HOH A 81 2081 2081 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 O O3B CDP . . . B 2 54.161 43.497 2.624 1 38.85 ? O3B CDP 1374 A 1 HETATM 2 P PB CDP . . . B 2 55.038 43.94 1.307 1 37.03 ? PB CDP 1374 A 1 HETATM 3 O O1B CDP . . . B 2 54.556 43.02 0.164 1 37.41 ? O1B CDP 1374 A 1 HETATM 4 O O2B CDP . . . B 2 54.769 45.334 0.861 1 38.6 ? O2B CDP 1374 A 1 HETATM 5 O O3A CDP . . . B 2 56.604 43.577 1.602 1 37 ? O3A CDP 1374 A 1 HETATM 6 P PA CDP . . . B 2 56.952 42.017 1.746 1 37.31 ? PA CDP 1374 A 1 HETATM 7 O O1A CDP . . . B 2 58.415 41.907 1.022 1 34.68 ? O1A CDP 1374 A 1 HETATM 8 O O2A CDP . . . B 2 56.906 41.534 3.177 1 37.23 ? O2A CDP 1374 A 1 HETATM 9 O O5' CDP . . . B 2 55.803 41.255 0.726 1 35.43 ? O5' CDP 1374 A 1 HETATM 10 C C5' CDP . . . B 2 54.401 40.748 1.132 1 28.52 ? C5' CDP 1374 A 1 HETATM 11 C C4' CDP . . . B 2 53.416 40.328 -0.049 1 21.57 ? C4' CDP 1374 A 1 HETATM 12 O O4' CDP . . . B 2 53.856 40.773 -1.334 1 18.72 ? O4' CDP 1374 A 1 HETATM 13 C C3' CDP . . . B 2 53.386 38.821 -0.2 1 19.31 ? C3' CDP 1374 A 1 HETATM 14 O O3' CDP . . . B 2 52.43 38.246 0.677 1 18.96 ? O3' CDP 1374 A 1 HETATM 15 C C2' CDP . . . B 2 53.048 38.572 -1.678 1 18.89 ? C2' CDP 1374 A 1 HETATM 16 O O2' CDP . . . B 2 51.668 38.48 -2.023 1 16.67 ? O2' CDP 1374 A 1 HETATM 17 C C1' CDP . . . B 2 53.474 39.834 -2.324 1 18.22 ? C1' CDP 1374 A 1 HETATM 18 N N1 CDP . . . B 2 54.678 39.6 -3.109 1 19.27 ? N1 CDP 1374 A 1 HETATM 19 C C2 CDP . . . B 2 54.571 39.184 -4.41 1 19.45 ? C2 CDP 1374 A 1 HETATM 20 O O2 CDP . . . B 2 53.459 38.951 -4.896 1 21.27 ? O2 CDP 1374 A 1 HETATM 21 N N3 CDP . . . B 2 55.736 39.025 -5.158 1 18.83 ? N3 CDP 1374 A 1 HETATM 22 C C4 CDP . . . B 2 56.983 39.28 -4.638 1 16.9 ? C4 CDP 1374 A 1 HETATM 23 N N4 CDP . . . B 2 58.065 39.141 -5.372 1 17.32 ? N4 CDP 1374 A 1 HETATM 24 C C5 CDP . . . B 2 57.094 39.695 -3.343 1 19.2 ? C5 CDP 1374 A 1 HETATM 25 C C6 CDP . . . B 2 55.938 39.872 -2.582 1 20.94 ? C6 CDP 1374 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 247 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #