data_2NG1 # _model_server_result.job_id 46i5yh0fDo0tcT9Y9sCJmw _model_server_result.datetime_utc '2024-10-12 12:21:02' _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 2ng1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":900}' # _entry.id 2NG1 # _exptl.entry_id 2NG1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _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 119.62 _cell.angle_gamma 90 _cell.entry_id 2NG1 _cell.length_a 110.425 _cell.length_b 54.214 _cell.length_c 58.465 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2NG1 _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 '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 93 n n PB O2B GDP sing 94 n n PB O3B GDP sing 95 n n PB O3A GDP sing 96 n n O2B HOB2 GDP sing 97 n n O3B HOB3 GDP sing 98 n n O3A PA GDP sing 99 n n PA O1A GDP doub 100 n n PA O2A GDP sing 101 n n PA O5' GDP sing 102 n n O2A HOA2 GDP sing 103 n n O5' C5' GDP sing 104 n n C5' C4' GDP sing 105 n n C5' H5' GDP sing 106 n n C5' "H5''" GDP sing 107 n n C4' O4' GDP sing 108 n n C4' C3' GDP sing 109 n n C4' H4' GDP sing 110 n n O4' C1' GDP sing 111 n n C3' O3' GDP sing 112 n n C3' C2' GDP sing 113 n n C3' H3' GDP sing 114 n n O3' HO3' GDP sing 115 n n C2' O2' GDP sing 116 n n C2' C1' GDP sing 117 n n C2' H2' GDP sing 118 n n O2' HO2' GDP sing 119 n n C1' N9 GDP sing 120 n n C1' H1' GDP sing 121 n n N9 C8 GDP sing 122 n y N9 C4 GDP sing 123 n y C8 N7 GDP doub 124 n y C8 H8 GDP sing 125 n n N7 C5 GDP sing 126 n y C5 C6 GDP sing 127 n n C5 C4 GDP doub 128 n y C6 O6 GDP doub 129 n n C6 N1 GDP sing 130 n n N1 C2 GDP sing 131 n n N1 HN1 GDP sing 132 n n C2 N2 GDP sing 133 n n C2 N3 GDP doub 134 n n N2 HN21 GDP sing 135 n n N2 HN22 GDP sing 136 n n N3 C4 GDP sing 137 n n # _atom_sites.entry_id 2NG1 _atom_sites.fract_transf_matrix[1][1] 0.009056 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005149 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018445 _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] 0.019675 _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 GDP A 1 900 900 GDP GDP . C 3 DIO A 1 800 800 DIO DOX . D 4 EDO A 1 971 971 EDO EDO . E 4 EDO A 1 973 973 EDO EDO . F 5 HOH A 1 974 1 HOH HOH . F 5 HOH A 2 975 2 HOH HOH . F 5 HOH A 3 976 3 HOH HOH . F 5 HOH A 4 977 4 HOH HOH . F 5 HOH A 5 978 5 HOH HOH . F 5 HOH A 6 979 7 HOH HOH . F 5 HOH A 7 980 8 HOH HOH . F 5 HOH A 8 981 9 HOH HOH . F 5 HOH A 9 982 10 HOH HOH . F 5 HOH A 10 983 11 HOH HOH . F 5 HOH A 11 984 12 HOH HOH . F 5 HOH A 12 985 13 HOH HOH . F 5 HOH A 13 986 15 HOH HOH . F 5 HOH A 14 987 17 HOH HOH . F 5 HOH A 15 988 18 HOH HOH . F 5 HOH A 16 989 19 HOH HOH . F 5 HOH A 17 990 20 HOH HOH . F 5 HOH A 18 991 22 HOH HOH . F 5 HOH A 19 992 23 HOH HOH . F 5 HOH A 20 993 24 HOH HOH . F 5 HOH A 21 994 25 HOH HOH . F 5 HOH A 22 995 26 HOH HOH . F 5 HOH A 23 996 27 HOH HOH . F 5 HOH A 24 997 28 HOH HOH . F 5 HOH A 25 998 29 HOH HOH . F 5 HOH A 26 999 30 HOH HOH . F 5 HOH A 27 1000 31 HOH HOH . F 5 HOH A 28 1001 33 HOH HOH . F 5 HOH A 29 1002 37 HOH HOH . F 5 HOH A 30 1003 38 HOH HOH . F 5 HOH A 31 1004 39 HOH HOH . F 5 HOH A 32 1005 40 HOH HOH . F 5 HOH A 33 1006 41 HOH HOH . F 5 HOH A 34 1007 42 HOH HOH . F 5 HOH A 35 1008 43 HOH HOH . F 5 HOH A 36 1009 44 HOH HOH . F 5 HOH A 37 1010 45 HOH HOH . F 5 HOH A 38 1011 46 HOH HOH . F 5 HOH A 39 1012 47 HOH HOH . F 5 HOH A 40 1013 48 HOH HOH . F 5 HOH A 41 1014 49 HOH HOH . F 5 HOH A 42 1015 51 HOH HOH . F 5 HOH A 43 1016 52 HOH HOH . F 5 HOH A 44 1017 53 HOH HOH . F 5 HOH A 45 1018 54 HOH HOH . F 5 HOH A 46 1019 55 HOH HOH . F 5 HOH A 47 1020 56 HOH HOH . F 5 HOH A 48 1021 57 HOH HOH . F 5 HOH A 49 1022 58 HOH HOH . F 5 HOH A 50 1023 59 HOH HOH . F 5 HOH A 51 1024 60 HOH HOH . F 5 HOH A 52 1025 63 HOH HOH . F 5 HOH A 53 1026 64 HOH HOH . F 5 HOH A 54 1027 65 HOH HOH . F 5 HOH A 55 1028 66 HOH HOH . F 5 HOH A 56 1029 67 HOH HOH . F 5 HOH A 57 1030 68 HOH HOH . F 5 HOH A 58 1031 69 HOH HOH . F 5 HOH A 59 1032 70 HOH HOH . F 5 HOH A 60 1033 71 HOH HOH . F 5 HOH A 61 1034 72 HOH HOH . F 5 HOH A 62 1035 73 HOH HOH . F 5 HOH A 63 1036 74 HOH HOH . F 5 HOH A 64 1037 75 HOH HOH . F 5 HOH A 65 1038 76 HOH HOH . F 5 HOH A 66 1039 77 HOH HOH . F 5 HOH A 67 1040 78 HOH HOH . F 5 HOH A 68 1041 79 HOH HOH . F 5 HOH A 69 1042 80 HOH HOH . F 5 HOH A 70 1043 81 HOH HOH . F 5 HOH A 71 1044 82 HOH HOH . F 5 HOH A 72 1045 83 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 . . . B 2 -21.677 -3.984 13.893 1 40.1 ? PB GDP 900 A 1 HETATM 2 O O1B GDP . . . B 2 -21.012 -4.473 12.67 1 39.46 ? O1B GDP 900 A 1 HETATM 3 O O2B GDP . . . B 2 -21.343 -4.79 15.107 1 39.49 ? O2B GDP 900 A 1 HETATM 4 O O3B GDP . . . B 2 -23.118 -3.709 13.735 1 36.58 ? O3B GDP 900 A 1 HETATM 5 O O3A GDP . . . B 2 -21.06 -2.552 14.157 1 31.33 ? O3A GDP 900 A 1 HETATM 6 P PA GDP . . . B 2 -19.612 -1.881 14.044 1 32.52 ? PA GDP 900 A 1 HETATM 7 O O1A GDP . . . B 2 -19.682 -0.72 13.168 1 27.55 ? O1A GDP 900 A 1 HETATM 8 O O2A GDP . . . B 2 -18.641 -2.951 13.77 1 32.09 ? O2A GDP 900 A 1 HETATM 9 O O5' GDP . . . B 2 -19.382 -1.322 15.512 1 38.27 ? O5' GDP 900 A 1 HETATM 10 C C5' GDP . . . B 2 -19.276 -2.201 16.63 1 29.59 ? C5' GDP 900 A 1 HETATM 11 C C4' GDP . . . B 2 -19.554 -1.411 17.947 1 27.91 ? C4' GDP 900 A 1 HETATM 12 O O4' GDP . . . B 2 -18.351 -0.765 18.338 1 25.78 ? O4' GDP 900 A 1 HETATM 13 C C3' GDP . . . B 2 -20.598 -0.255 17.935 1 25.92 ? C3' GDP 900 A 1 HETATM 14 O O3' GDP . . . B 2 -21.39 -0.276 19.115 1 25.01 ? O3' GDP 900 A 1 HETATM 15 C C2' GDP . . . B 2 -19.791 1.037 17.84 1 25.96 ? C2' GDP 900 A 1 HETATM 16 O O2' GDP . . . B 2 -20.37 2.223 18.357 1 28.42 ? O2' GDP 900 A 1 HETATM 17 C C1' GDP . . . B 2 -18.588 0.645 18.616 1 26.15 ? C1' GDP 900 A 1 HETATM 18 N N9 GDP . . . B 2 -17.342 1.333 18.269 1 25.94 ? N9 GDP 900 A 1 HETATM 19 C C8 GDP . . . B 2 -16.744 1.482 17.028 1 22.84 ? C8 GDP 900 A 1 HETATM 20 N N7 GDP . . . B 2 -15.633 2.132 17.035 1 22.79 ? N7 GDP 900 A 1 HETATM 21 C C5 GDP . . . B 2 -15.448 2.445 18.405 1 26.15 ? C5 GDP 900 A 1 HETATM 22 C C6 GDP . . . B 2 -14.377 3.149 19.066 1 26.59 ? C6 GDP 900 A 1 HETATM 23 O O6 GDP . . . B 2 -13.372 3.629 18.529 1 24.82 ? O6 GDP 900 A 1 HETATM 24 N N1 GDP . . . B 2 -14.571 3.271 20.47 1 18.67 ? N1 GDP 900 A 1 HETATM 25 C C2 GDP . . . B 2 -15.661 2.765 21.168 1 26.8 ? C2 GDP 900 A 1 HETATM 26 N N2 GDP . . . B 2 -15.715 2.947 22.489 1 20.87 ? N2 GDP 900 A 1 HETATM 27 N N3 GDP . . . B 2 -16.667 2.087 20.554 1 29.4 ? N3 GDP 900 A 1 HETATM 28 C C4 GDP . . . B 2 -16.492 1.969 19.168 1 29.89 ? C4 GDP 900 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 261 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #