data_2CVV # _model_server_result.job_id lRqSbYjj4CREwcCsEoPgWg _model_server_result.datetime_utc '2024-12-02 04:59:35' _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 2cvv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1002}' # _entry.id 2CVV # _exptl.entry_id 2CVV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-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 2CVV _cell.length_a 107.866 _cell.length_b 117.593 _cell.length_c 64.884 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2CVV _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 ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_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_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 0 117.593 0 # _struct_asym.details ? _struct_asym.entity_id 4 _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 C O2A ANP . A ANP 1001 1_555 B MG MG . A MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc2 C O2B ANP . A ANP 1001 1_555 B MG MG . A MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.472 ? metalc ? metalc3 C O2G ANP . A ANP 1001 1_555 B MG MG . A MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? # _chem_comp.formula 'C9 H14 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id UDP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE" _chem_comp.type 'rna 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 UDP sing 408 n n N1 C6 UDP sing 409 n n N1 C1' UDP sing 410 n n C2 N3 UDP sing 411 n n C2 O2 UDP doub 412 n n N3 C4 UDP sing 413 n n N3 HN3 UDP sing 414 n n C4 C5 UDP sing 415 n n C4 O4 UDP doub 416 n n C5 C6 UDP doub 417 n n C5 H5 UDP sing 418 n n C6 H6 UDP sing 419 n n C1' C2' UDP sing 420 n n C1' O4' UDP sing 421 n n C1' H1' UDP sing 422 n n C2' O2' UDP sing 423 n n C2' C3' UDP sing 424 n n C2' H2' UDP sing 425 n n O2' HO2' UDP sing 426 n n C3' C4' UDP sing 427 n n C3' O3' UDP sing 428 n n C3' H3' UDP sing 429 n n C4' O4' UDP sing 430 n n C4' C5' UDP sing 431 n n C4' H4' UDP sing 432 n n O3' HO3' UDP sing 433 n n C5' O5' UDP sing 434 n n C5' "H5'1" UDP sing 435 n n C5' "H5'2" UDP sing 436 n n O5' PA UDP sing 437 n n PA O1A UDP doub 438 n n PA O2A UDP sing 439 n n PA O3A UDP sing 440 n n O2A HOA2 UDP sing 441 n n O3A PB UDP sing 442 n n PB O1B UDP doub 443 n n PB O2B UDP sing 444 n n PB O3B UDP sing 445 n n O2B HOB2 UDP sing 446 n n O3B HOB3 UDP sing 447 n n # _atom_sites.entry_id 2CVV _atom_sites.fract_transf_matrix[1][1] 0.009271 _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] 0.008504 _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] 0.015412 _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 MG A 1 2001 2001 MG MG . C 3 ANP A 1 1001 1001 ANP ANP . D 4 UDP A 1 1002 1002 UDP UDP . E 5 HOH A 1 2002 1 HOH HOH . E 5 HOH A 2 2003 2 HOH HOH . E 5 HOH A 3 2004 3 HOH HOH . E 5 HOH A 4 2005 4 HOH HOH . E 5 HOH A 5 2006 5 HOH HOH . E 5 HOH A 6 2007 6 HOH HOH . E 5 HOH A 7 2008 7 HOH HOH . E 5 HOH A 8 2009 8 HOH HOH . E 5 HOH A 9 2010 9 HOH HOH . E 5 HOH A 10 2011 10 HOH HOH . E 5 HOH A 11 2012 11 HOH HOH . E 5 HOH A 12 2013 12 HOH HOH . E 5 HOH A 13 2014 13 HOH HOH . E 5 HOH A 14 2015 14 HOH HOH . E 5 HOH A 15 2016 15 HOH HOH . E 5 HOH A 16 2017 16 HOH HOH . E 5 HOH A 17 2018 17 HOH HOH . E 5 HOH A 18 2019 18 HOH HOH . E 5 HOH A 19 2020 19 HOH HOH . E 5 HOH A 20 2021 20 HOH HOH . E 5 HOH A 21 2022 21 HOH HOH . E 5 HOH A 22 2023 22 HOH HOH . E 5 HOH A 23 2024 23 HOH HOH . E 5 HOH A 24 2025 24 HOH HOH . E 5 HOH A 25 2026 25 HOH HOH . E 5 HOH A 26 2027 26 HOH HOH . E 5 HOH A 27 2028 27 HOH HOH . E 5 HOH A 28 2029 28 HOH HOH . E 5 HOH A 29 2030 29 HOH HOH . E 5 HOH A 30 2031 30 HOH HOH . E 5 HOH A 31 2032 31 HOH HOH . E 5 HOH A 32 2033 32 HOH HOH . E 5 HOH A 33 2034 33 HOH HOH . E 5 HOH A 34 2035 34 HOH HOH . E 5 HOH A 35 2036 35 HOH HOH . E 5 HOH A 36 2037 36 HOH HOH . E 5 HOH A 37 2038 37 HOH HOH . E 5 HOH A 38 2039 38 HOH HOH . E 5 HOH A 39 2040 39 HOH HOH . E 5 HOH A 40 2041 40 HOH HOH . E 5 HOH A 41 2042 41 HOH HOH . E 5 HOH A 42 2043 42 HOH HOH . E 5 HOH A 43 2044 43 HOH HOH . E 5 HOH A 44 2045 44 HOH HOH . E 5 HOH A 45 2046 45 HOH HOH . E 5 HOH A 46 2047 46 HOH HOH . E 5 HOH A 47 2048 47 HOH HOH . E 5 HOH A 48 2049 48 HOH HOH . E 5 HOH A 49 2050 49 HOH HOH . E 5 HOH A 50 2051 50 HOH HOH . E 5 HOH A 51 2052 51 HOH HOH . E 5 HOH A 52 2053 52 HOH HOH . E 5 HOH A 53 2054 53 HOH HOH . E 5 HOH A 54 2055 54 HOH HOH . E 5 HOH A 55 2056 55 HOH HOH . E 5 HOH A 56 2057 56 HOH HOH . E 5 HOH A 57 2058 57 HOH HOH . E 5 HOH A 58 2059 58 HOH HOH . E 5 HOH A 59 2060 59 HOH HOH . E 5 HOH A 60 2061 60 HOH HOH . E 5 HOH A 61 2062 61 HOH HOH . E 5 HOH A 62 2063 62 HOH HOH . E 5 HOH A 63 2064 63 HOH HOH . E 5 HOH A 64 2065 64 HOH HOH . E 5 HOH A 65 2066 65 HOH HOH . E 5 HOH A 66 2067 66 HOH HOH . E 5 HOH A 67 2068 67 HOH HOH . E 5 HOH A 68 2069 68 HOH HOH . E 5 HOH A 69 2070 69 HOH HOH . E 5 HOH A 70 2071 70 HOH HOH . E 5 HOH A 71 2072 71 HOH HOH . E 5 HOH A 72 2073 72 HOH HOH . E 5 HOH A 73 2074 73 HOH HOH . E 5 HOH A 74 2075 74 HOH HOH . E 5 HOH A 75 2076 75 HOH HOH . E 5 HOH A 76 2077 76 HOH HOH . E 5 HOH A 77 2078 77 HOH HOH . E 5 HOH A 78 2079 78 HOH HOH . E 5 HOH A 79 2080 79 HOH HOH . E 5 HOH A 80 2081 80 HOH HOH . E 5 HOH A 81 2082 81 HOH HOH . E 5 HOH A 82 2083 82 HOH HOH . E 5 HOH A 83 2084 83 HOH HOH . E 5 HOH A 84 2085 84 HOH HOH . E 5 HOH A 85 2086 85 HOH HOH . E 5 HOH A 86 2087 86 HOH HOH . E 5 HOH A 87 2088 87 HOH HOH . E 5 HOH A 88 2089 88 HOH HOH . E 5 HOH A 89 2090 89 HOH HOH . E 5 HOH A 90 2091 90 HOH HOH . E 5 HOH A 91 2092 91 HOH HOH . E 5 HOH A 92 2093 92 HOH HOH . E 5 HOH A 93 2094 93 HOH HOH . E 5 HOH A 94 2095 94 HOH HOH . E 5 HOH A 95 2096 95 HOH HOH . E 5 HOH A 96 2097 96 HOH HOH . E 5 HOH A 97 2098 97 HOH HOH . E 5 HOH A 98 2099 98 HOH HOH . E 5 HOH A 99 2100 99 HOH HOH . E 5 HOH A 100 2101 100 HOH HOH . E 5 HOH A 101 2102 101 HOH HOH . E 5 HOH A 102 2103 102 HOH HOH . E 5 HOH A 103 2104 103 HOH HOH . E 5 HOH A 104 2105 104 HOH HOH . E 5 HOH A 105 2106 105 HOH HOH . E 5 HOH A 106 2107 106 HOH HOH . E 5 HOH A 107 2108 107 HOH HOH . E 5 HOH A 108 2109 108 HOH HOH . E 5 HOH A 109 2110 109 HOH HOH . E 5 HOH A 110 2111 110 HOH HOH . E 5 HOH A 111 2112 111 HOH HOH . E 5 HOH A 112 2113 112 HOH HOH . E 5 HOH A 113 2114 113 HOH HOH . E 5 HOH A 114 2115 114 HOH HOH . E 5 HOH A 115 2116 115 HOH HOH . E 5 HOH A 116 2117 116 HOH HOH . E 5 HOH A 117 2118 117 HOH HOH . E 5 HOH A 118 2119 118 HOH HOH . E 5 HOH A 119 2120 119 HOH HOH . E 5 HOH A 120 2121 120 HOH HOH . E 5 HOH A 121 2122 121 HOH HOH . E 5 HOH A 122 2123 122 HOH HOH . E 5 HOH A 123 2124 123 HOH HOH . E 5 HOH A 124 2125 124 HOH HOH . E 5 HOH A 125 2126 125 HOH HOH . E 5 HOH A 126 2127 126 HOH HOH . E 5 HOH A 127 2128 127 HOH HOH . E 5 HOH A 128 2129 128 HOH HOH . E 5 HOH A 129 2130 129 HOH HOH . E 5 HOH A 130 2131 130 HOH HOH . E 5 HOH A 131 2132 131 HOH HOH . E 5 HOH A 132 2133 132 HOH HOH . E 5 HOH A 133 2134 133 HOH HOH . E 5 HOH A 134 2135 134 HOH HOH . E 5 HOH A 135 2136 135 HOH HOH . E 5 HOH A 136 2137 136 HOH HOH . E 5 HOH A 137 2138 137 HOH HOH . E 5 HOH A 138 2139 138 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 UDP . . . D 4 20.96 52.137 16.637 1 57.14 ? N1 UDP 1002 A 1 HETATM 2 C C2 UDP . . . D 4 20.037 53.153 16.32 1 57.73 ? C2 UDP 1002 A 1 HETATM 3 N N3 UDP . . . D 4 20.002 53.637 15.007 1 58.04 ? N3 UDP 1002 A 1 HETATM 4 C C4 UDP . . . D 4 20.858 53.128 14.026 1 58.19 ? C4 UDP 1002 A 1 HETATM 5 C C5 UDP . . . D 4 21.758 52.126 14.369 1 57.57 ? C5 UDP 1002 A 1 HETATM 6 C C6 UDP . . . D 4 21.765 51.669 15.63 1 57.1 ? C6 UDP 1002 A 1 HETATM 7 O O2 UDP . . . D 4 19.26 53.64 17.163 1 56.86 ? O2 UDP 1002 A 1 HETATM 8 O O4 UDP . . . D 4 20.842 53.551 12.865 1 58.8 ? O4 UDP 1002 A 1 HETATM 9 C C1' UDP . . . D 4 21.067 51.53 18.005 1 55.89 ? C1' UDP 1002 A 1 HETATM 10 C C2' UDP . . . D 4 20.288 50.209 18.106 1 54.42 ? C2' UDP 1002 A 1 HETATM 11 O O2' UDP . . . D 4 19.586 50.089 19.329 1 51.34 ? O2' UDP 1002 A 1 HETATM 12 C C3' UDP . . . D 4 21.368 49.14 17.986 1 54.8 ? C3' UDP 1002 A 1 HETATM 13 C C4' UDP . . . D 4 22.633 49.818 18.495 1 54.51 ? C4' UDP 1002 A 1 HETATM 14 O O4' UDP . . . D 4 22.421 51.22 18.34 1 55.47 ? O4' UDP 1002 A 1 HETATM 15 O O3' UDP . . . D 4 21.077 47.942 18.679 1 55.63 ? O3' UDP 1002 A 1 HETATM 16 C C5' UDP . . . D 4 23.874 49.364 17.727 1 52.46 ? C5' UDP 1002 A 1 HETATM 17 O O5' UDP . . . D 4 24.095 50.243 16.645 1 49.67 ? O5' UDP 1002 A 1 HETATM 18 P PA UDP . . . D 4 25.481 50.363 15.832 1 47.81 ? PA UDP 1002 A 1 HETATM 19 O O1A UDP . . . D 4 26.548 49.528 16.444 1 47.79 ? O1A UDP 1002 A 1 HETATM 20 O O2A UDP . . . D 4 25.242 50.047 14.391 1 47.4 ? O2A UDP 1002 A 1 HETATM 21 O O3A UDP . . . D 4 25.807 51.943 15.971 1 46.09 ? O3A UDP 1002 A 1 HETATM 22 P PB UDP . . . D 4 27.117 52.655 16.6 1 42.18 ? PB UDP 1002 A 1 HETATM 23 O O1B UDP . . . D 4 28.341 52.051 16.011 1 43.22 ? O1B UDP 1002 A 1 HETATM 24 O O2B UDP . . . D 4 27.098 54.083 16.21 1 40.49 ? O2B UDP 1002 A 1 HETATM 25 O O3B UDP . . . D 4 27.073 52.485 18.066 1 41.47 ? O3B UDP 1002 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 14 _model_server_stats.element_count 25 #