data_2CVW # _model_server_result.job_id EsCHEDqoge0lhOR8DZvzmg _model_server_result.datetime_utc '2024-12-04 01:41:05' _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 2cvw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1002}' # _entry.id 2CVW # _exptl.entry_id 2CVW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-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 2CVW _cell.length_a 107.526 _cell.length_b 117.389 _cell.length_c 64.831 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2CVW _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 0 117.389 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 O3B TTP . A TTP 1001 1_555 B MG MG . A MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? metalc ? metalc2 C O3A TTP . A TTP 1001 1_555 B MG MG . A MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc3 C O2B TTP . A TTP 1001 1_555 B MG MG . A MG 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-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 PB O1B GDP doub 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 2CVW _atom_sites.fract_transf_matrix[1][1] 0.0093 _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] 0.008519 _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] 0.015425 _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 TTP A 1 1001 1001 TTP TTP . D 4 GDP A 1 1002 1002 GDP GDP . 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 . # 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 P PB GDP . . . D 4 26.681 52.735 16.888 1 43.69 ? PB GDP 1002 A 1 HETATM 2 O O1B GDP . . . D 4 28.098 52.41 17.175 1 42.79 ? O1B GDP 1002 A 1 HETATM 3 O O2B GDP . . . D 4 25.839 52.672 18.162 1 47.7 ? O2B GDP 1002 A 1 HETATM 4 O O3B GDP . . . D 4 26.61 54.088 16.215 1 44.44 ? O3B GDP 1002 A 1 HETATM 5 O O3A GDP . . . D 4 26.057 51.741 15.782 1 47.89 ? O3A GDP 1002 A 1 HETATM 6 P PA GDP . . . D 4 25.487 50.228 15.882 1 46.56 ? PA GDP 1002 A 1 HETATM 7 O O1A GDP . . . D 4 24.922 49.941 14.524 1 46.55 ? O1A GDP 1002 A 1 HETATM 8 O O2A GDP . . . D 4 26.601 49.277 16.272 1 48.23 ? O2A GDP 1002 A 1 HETATM 9 O O5' GDP . . . D 4 24.348 50.321 16.994 1 46.51 ? O5' GDP 1002 A 1 HETATM 10 C C5' GDP . . . D 4 23.985 49.231 17.831 1 43.77 ? C5' GDP 1002 A 1 HETATM 11 C C4' GDP . . . D 4 22.799 49.688 18.673 1 43.77 ? C4' GDP 1002 A 1 HETATM 12 O O4' GDP . . . D 4 22.553 51.097 18.539 1 43.4 ? O4' GDP 1002 A 1 HETATM 13 C C3' GDP . . . D 4 21.536 48.958 18.253 1 42.37 ? C3' GDP 1002 A 1 HETATM 14 O O3' GDP . . . D 4 21.318 47.875 19.146 1 42.39 ? O3' GDP 1002 A 1 HETATM 15 C C2' GDP . . . D 4 20.437 50.02 18.219 1 42.3 ? C2' GDP 1002 A 1 HETATM 16 O O2' GDP . . . D 4 19.508 50.006 19.298 1 36.79 ? O2' GDP 1002 A 1 HETATM 17 C C1' GDP . . . D 4 21.198 51.346 18.159 1 45.71 ? C1' GDP 1002 A 1 HETATM 18 N N9 GDP . . . D 4 21.078 51.801 16.745 1 46.41 ? N9 GDP 1002 A 1 HETATM 19 C C8 GDP . . . D 4 21.797 51.386 15.676 1 46.75 ? C8 GDP 1002 A 1 HETATM 20 N N7 GDP . . . D 4 21.373 52.004 14.533 1 48.33 ? N7 GDP 1002 A 1 HETATM 21 C C5 GDP . . . D 4 20.364 52.827 14.881 1 47.43 ? C5 GDP 1002 A 1 HETATM 22 C C6 GDP . . . D 4 19.47 53.767 14.168 1 48.03 ? C6 GDP 1002 A 1 HETATM 23 O O6 GDP . . . D 4 19.627 53.893 12.927 1 48.2 ? O6 GDP 1002 A 1 HETATM 24 N N1 GDP . . . D 4 18.526 54.435 14.886 1 47.28 ? N1 GDP 1002 A 1 HETATM 25 C C2 GDP . . . D 4 18.397 54.258 16.242 1 47.48 ? C2 GDP 1002 A 1 HETATM 26 N N2 GDP . . . D 4 17.454 54.942 16.934 1 46.02 ? N2 GDP 1002 A 1 HETATM 27 N N3 GDP . . . D 4 19.189 53.406 16.952 1 45.83 ? N3 GDP 1002 A 1 HETATM 28 C C4 GDP . . . D 4 20.161 52.681 16.336 1 46.97 ? C4 GDP 1002 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #