data_4C81 # _model_server_result.job_id XwTNBgbMoKBGy9HbOCfxyg _model_server_result.datetime_utc '2024-10-18 23:30:43' _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 4c81 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1242}' # _entry.id 4C81 # _exptl.entry_id 4C81 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 403.176 _entity.id 3 _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 120 _cell.entry_id 4C81 _cell.length_a 84.864 _cell.length_b 84.864 _cell.length_c 101.031 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4C81 _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 1,2,3 # 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_455 -y-1,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -84.864 0 0 3 'crystal symmetry operation' 3_445 -x+y-1,-x-1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -42.432 -73.49438 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _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 metalc ? metalc1 A OD2 ASP 15 A ASP 71 1_555 B ZN ZN . A ZN 1240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc2 A NE2 HIS 17 A HIS 73 1_555 B ZN ZN . A ZN 1240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc3 A ND1 HIS 67 A HIS 123 1_555 B ZN ZN . A ZN 1240 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc4 A NE2 HIS 159 A HIS 215 1_555 C ZN ZN . A ZN 1241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc5 A OE1 GLU 172 A GLU 228 2_455 C ZN ZN . A ZN 1241 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc6 B ZN ZN . A ZN 1240 1_555 I O HOH . A HOH 2009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.821 ? metalc ? metalc7 C ZN ZN . A ZN 1241 1_555 E CL CL . A CL 1244 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc8 C ZN ZN . A ZN 1241 1_555 G CL CL . A CL 1246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.302 ? # _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 70 n n PB O1B CDP doub 71 n n PB O2B CDP sing 72 n n PB O3A CDP sing 73 n n O3A PA CDP sing 74 n n PA O1A CDP doub 75 n n PA O2A CDP sing 76 n n PA O5' CDP sing 77 n n O5' C5' CDP sing 78 n n C5' C4' CDP sing 79 n n C5' "H5'1" CDP sing 80 n n C5' "H5'2" CDP sing 81 n n C4' O4' CDP sing 82 n n C4' C3' CDP sing 83 n n C4' H4' CDP sing 84 n n O4' C1' CDP sing 85 n n C3' O3' CDP sing 86 n n C3' C2' CDP sing 87 n n C3' H3' CDP sing 88 n n O3' HA CDP sing 89 n n C2' O2' CDP sing 90 n n C2' C1' CDP sing 91 n n C2' H2' CDP sing 92 n n O2' HB CDP sing 93 n n C1' N1 CDP sing 94 n n C1' H1' CDP sing 95 n n N1 C2 CDP sing 96 n n N1 C6 CDP sing 97 n n C2 O2 CDP doub 98 n n C2 N3 CDP sing 99 n n N3 C4 CDP doub 100 n n C4 N4 CDP sing 101 n n C4 C5 CDP sing 102 n n N4 H4N1 CDP sing 103 n n N4 H4N2 CDP sing 104 n n C5 C6 CDP doub 105 n n C5 H5 CDP sing 106 n n C6 H6 CDP sing 107 n n HO1 O2A CDP sing 108 n n HO2 O2B CDP sing 109 n n HO3 O3B CDP sing 110 n n # _atom_sites.entry_id 4C81 _atom_sites.fract_transf_matrix[1][1] 0.011784 _atom_sites.fract_transf_matrix[1][2] 0.006803 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013606 _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] 0.009898 _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 ZN A 1 1240 1240 ZN ZN . C 2 ZN A 1 1241 1241 ZN ZN . D 3 CDP A 1 1242 1242 CDP CDP . E 4 CL A 1 1244 1244 CL CL . F 4 CL A 1 1245 1245 CL CL . G 4 CL A 1 1246 1246 CL CL . H 5 SO4 A 1 1247 1247 SO4 SO4 . I 6 HOH A 1 2001 2001 HOH HOH . I 6 HOH A 2 2002 2002 HOH HOH . I 6 HOH A 3 2003 2003 HOH HOH . I 6 HOH A 4 2004 2004 HOH HOH . I 6 HOH A 5 2005 2005 HOH HOH . I 6 HOH A 6 2006 2006 HOH HOH . I 6 HOH A 7 2007 2007 HOH HOH . I 6 HOH A 8 2008 2008 HOH HOH . I 6 HOH A 9 2009 2009 HOH HOH . I 6 HOH A 10 2010 2010 HOH HOH . I 6 HOH A 11 2011 2011 HOH HOH . I 6 HOH A 12 2012 2012 HOH HOH . I 6 HOH A 13 2013 2013 HOH HOH . I 6 HOH A 14 2014 2014 HOH HOH . I 6 HOH A 15 2015 2015 HOH HOH . I 6 HOH A 16 2016 2016 HOH HOH . I 6 HOH A 17 2017 2017 HOH HOH . I 6 HOH A 18 2018 2018 HOH HOH . I 6 HOH A 19 2019 2019 HOH HOH . I 6 HOH A 20 2020 2020 HOH HOH . I 6 HOH A 21 2021 2021 HOH HOH . I 6 HOH A 22 2022 2022 HOH HOH . I 6 HOH A 23 2023 2023 HOH HOH . I 6 HOH A 24 2024 2024 HOH HOH . I 6 HOH A 25 2025 2025 HOH HOH . I 6 HOH A 26 2026 2026 HOH HOH . I 6 HOH A 27 2027 2027 HOH HOH . I 6 HOH A 28 2028 2028 HOH HOH . I 6 HOH A 29 2029 2029 HOH HOH . I 6 HOH A 30 2030 2030 HOH HOH . I 6 HOH A 31 2031 2031 HOH HOH . I 6 HOH A 32 2032 2032 HOH HOH . I 6 HOH A 33 2033 2033 HOH HOH . I 6 HOH A 34 2034 2034 HOH HOH . I 6 HOH A 35 2035 2035 HOH HOH . I 6 HOH A 36 2036 2036 HOH HOH . I 6 HOH A 37 2037 2037 HOH HOH . I 6 HOH A 38 2038 2038 HOH HOH . I 6 HOH A 39 2039 2039 HOH HOH . I 6 HOH A 40 2040 2040 HOH HOH . I 6 HOH A 41 2041 2041 HOH HOH . I 6 HOH A 42 2042 2042 HOH HOH . I 6 HOH A 43 2043 2043 HOH HOH . I 6 HOH A 44 2044 2044 HOH HOH . I 6 HOH A 45 2045 2045 HOH HOH . I 6 HOH A 46 2046 2046 HOH HOH . I 6 HOH A 47 2047 2047 HOH HOH . I 6 HOH A 48 2048 2048 HOH HOH . I 6 HOH A 49 2049 2049 HOH HOH . I 6 HOH A 50 2050 2050 HOH HOH . I 6 HOH A 51 2051 2051 HOH HOH . I 6 HOH A 52 2052 2052 HOH HOH . I 6 HOH A 53 2053 2053 HOH HOH . I 6 HOH A 54 2054 2054 HOH HOH . I 6 HOH A 55 2055 2055 HOH HOH . I 6 HOH A 56 2056 2056 HOH HOH . I 6 HOH A 57 2057 2057 HOH HOH . I 6 HOH A 58 2058 2058 HOH HOH . I 6 HOH A 59 2059 2059 HOH HOH . I 6 HOH A 60 2060 2060 HOH HOH . I 6 HOH A 61 2061 2061 HOH HOH . I 6 HOH A 62 2062 2062 HOH HOH . I 6 HOH A 63 2063 2063 HOH HOH . I 6 HOH A 64 2064 2064 HOH HOH . I 6 HOH A 65 2065 2065 HOH HOH . I 6 HOH A 66 2066 2066 HOH HOH . I 6 HOH A 67 2067 2067 HOH HOH . I 6 HOH A 68 2068 2068 HOH HOH . I 6 HOH A 69 2069 2069 HOH HOH . I 6 HOH A 70 2070 2070 HOH HOH . I 6 HOH A 71 2071 2071 HOH HOH . I 6 HOH A 72 2072 2072 HOH HOH . I 6 HOH A 73 2073 2073 HOH HOH . I 6 HOH A 74 2074 2074 HOH HOH . I 6 HOH A 75 2075 2075 HOH HOH . I 6 HOH A 76 2076 2076 HOH HOH . I 6 HOH A 77 2077 2077 HOH HOH . I 6 HOH A 78 2078 2078 HOH HOH . I 6 HOH A 79 2079 2079 HOH HOH . I 6 HOH A 80 2080 2080 HOH HOH . I 6 HOH A 81 2081 2081 HOH HOH . I 6 HOH A 82 2082 2082 HOH HOH . I 6 HOH A 83 2083 2083 HOH HOH . I 6 HOH A 84 2084 2084 HOH HOH . I 6 HOH A 85 2085 2085 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 . A . D 3 -27.736 -32.485 22.542 0.6 63.79 ? O3B CDP 1242 A 1 HETATM 2 O O3B CDP . B . D 3 -26.528 -35.378 22.888 0.4 26.15 ? O3B CDP 1242 A 1 HETATM 3 P PB CDP . A . D 3 -28.063 -32.793 20.984 0.6 55.94 ? PB CDP 1242 A 1 HETATM 4 P PB CDP . B . D 3 -27.43 -34.083 22.521 0.4 45.75 ? PB CDP 1242 A 1 HETATM 5 O O1B CDP . A . D 3 -28.079 -31.358 20.286 0.6 30.76 ? O1B CDP 1242 A 1 HETATM 6 O O1B CDP . B . D 3 -27.166 -33.033 23.724 0.4 45.88 ? O1B CDP 1242 A 1 HETATM 7 O O2B CDP . A . D 3 -27.056 -33.682 20.35 0.6 35.89 ? O2B CDP 1242 A 1 HETATM 8 O O2B CDP . B . D 3 -27.068 -33.508 21.201 0.4 63.53 ? O2B CDP 1242 A 1 HETATM 9 O O3A CDP . A . D 3 -29.583 -33.324 20.874 0.6 39.92 ? O3A CDP 1242 A 1 HETATM 10 O O3A CDP . B . D 3 -28.974 -34.541 22.63 0.4 71.81 ? O3A CDP 1242 A 1 HETATM 11 P PA CDP . A . D 3 -30.236 -34.428 21.854 0.6 28.07 ? PA CDP 1242 A 1 HETATM 12 P PA CDP . B . D 3 -30.034 -34.113 21.494 0.4 28.61 ? PA CDP 1242 A 1 HETATM 13 O O1A CDP . A . D 3 -29.373 -34.706 23.023 0.6 29.29 ? O1A CDP 1242 A 1 HETATM 14 O O1A CDP . B . D 3 -31.289 -33.674 22.144 0.4 23.74 ? O1A CDP 1242 A 1 HETATM 15 O O2A CDP . A . D 3 -31.641 -34.028 22.073 0.6 52.7 ? O2A CDP 1242 A 1 HETATM 16 O O2A CDP . B . D 3 -29.365 -33.23 20.513 0.4 42.84 ? O2A CDP 1242 A 1 HETATM 17 O O5' CDP . A . D 3 -30.258 -35.74 20.925 0.6 36.57 ? O5' CDP 1242 A 1 HETATM 18 O O5' CDP . B . D 3 -30.349 -35.517 20.772 0.4 18.03 ? O5' CDP 1242 A 1 HETATM 19 C C5' CDP . A . D 3 -29.171 -36.075 20.053 0.6 34.78 ? C5' CDP 1242 A 1 HETATM 20 C C5' CDP . B . D 3 -29.285 -36.385 20.393 0.4 17.12 ? C5' CDP 1242 A 1 HETATM 21 C C4' CDP . A . D 3 -29.63 -37.088 19.002 0.6 50.81 ? C4' CDP 1242 A 1 HETATM 22 C C4' CDP . B . D 3 -29.713 -37.273 19.237 0.4 15.84 ? C4' CDP 1242 A 1 HETATM 23 O O4' CDP . A . D 3 -30.338 -38.144 19.698 0.6 36.9 ? O4' CDP 1242 A 1 HETATM 24 O O4' CDP . B . D 3 -30.529 -38.36 19.719 0.4 16.66 ? O4' CDP 1242 A 1 HETATM 25 C C3' CDP . A . D 3 -30.668 -36.48 18.062 0.6 37.36 ? C3' CDP 1242 A 1 HETATM 26 C C3' CDP . B . D 3 -30.657 -36.476 18.352 0.4 22 ? C3' CDP 1242 A 1 HETATM 27 O O3' CDP . A . D 3 -30.029 -35.823 16.962 0.6 45.65 ? O3' CDP 1242 A 1 HETATM 28 O O3' CDP . B . D 3 -29.904 -35.639 17.472 0.4 18.82 ? O3' CDP 1242 A 1 HETATM 29 C C2' CDP . A . D 3 -31.411 -37.726 17.593 0.6 22.88 ? C2' CDP 1242 A 1 HETATM 30 C C2' CDP . B . D 3 -31.317 -37.61 17.591 0.4 17.9 ? C2' CDP 1242 A 1 HETATM 31 O O2' CDP . A . D 3 -30.682 -38.374 16.546 0.6 34.73 ? O2' CDP 1242 A 1 HETATM 32 O O2' CDP . B . D 3 -30.398 -38.156 16.643 0.4 14.68 ? O2' CDP 1242 A 1 HETATM 33 C C1' CDP . A . D 3 -31.412 -38.629 18.837 0.6 28.94 ? C1' CDP 1242 A 1 HETATM 34 C C1' CDP . B . D 3 -31.537 -38.632 18.705 0.4 18.88 ? C1' CDP 1242 A 1 HETATM 35 N N1 CDP . A . D 3 -32.755 -38.554 19.489 0.6 30.87 ? N1 CDP 1242 A 1 HETATM 36 N N1 CDP . B . D 3 -32.861 -38.385 19.309 0.4 11.55 ? N1 CDP 1242 A 1 HETATM 37 C C2 CDP . A . D 3 -33.844 -39.21 18.887 0.6 23.96 ? C2 CDP 1242 A 1 HETATM 38 C C2 CDP . B . D 3 -33.984 -39.089 18.863 0.4 12.56 ? C2 CDP 1242 A 1 HETATM 39 O O2 CDP . A . D 3 -33.697 -39.836 17.838 0.6 20.13 ? O2 CDP 1242 A 1 HETATM 40 O O2 CDP . B . D 3 -33.879 -39.92 17.963 0.4 24.73 ? O2 CDP 1242 A 1 HETATM 41 N N3 CDP . A . D 3 -35.102 -39.147 19.488 0.6 12.03 ? N3 CDP 1242 A 1 HETATM 42 N N3 CDP . B . D 3 -35.226 -38.836 19.451 0.4 58.2 ? N3 CDP 1242 A 1 HETATM 43 C C4 CDP . A . D 3 -35.307 -38.442 20.671 0.6 14.71 ? C4 CDP 1242 A 1 HETATM 44 C C4 CDP . B . D 3 -35.352 -37.896 20.469 0.4 16.33 ? C4 CDP 1242 A 1 HETATM 45 N N4 CDP . A . D 3 -36.526 -38.413 21.203 0.6 12.09 ? N4 CDP 1242 A 1 HETATM 46 N N4 CDP . B . D 3 -36.543 -37.67 21.013 0.4 57.4 ? N4 CDP 1242 A 1 HETATM 47 C C5 CDP . A . D 3 -34.237 -37.793 21.278 0.6 41.32 ? C5 CDP 1242 A 1 HETATM 48 C C5 CDP . B . D 3 -34.235 -37.203 20.906 0.4 7.48 ? C5 CDP 1242 A 1 HETATM 49 C C6 CDP . A . D 3 -32.971 -37.845 20.694 0.6 53.38 ? C6 CDP 1242 A 1 HETATM 50 C C6 CDP . B . D 3 -32.996 -37.443 20.327 0.4 7.29 ? C6 CDP 1242 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 50 #