data_5GOM # _model_server_result.job_id I7J9QPV-NuVkGPlT8w2n-Q _model_server_result.datetime_utc '2024-11-27 23:23:44' _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 5gom # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":901}' # _entry.id 5GOM # _exptl.entry_id 5GOM _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 92.23 _cell.angle_gamma 90 _cell.entry_id 5GOM _cell.length_a 146.108 _cell.length_b 45.982 _cell.length_c 146.18 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5GOM _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 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,F,G _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E N 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 100 n n PB O2B GDP sing 101 n n PB O3B GDP sing 102 n n PB O3A GDP sing 103 n n O2B HOB2 GDP sing 104 n n O3B HOB3 GDP sing 105 n n O3A PA GDP sing 106 n n PA O1A GDP doub 107 n n PA O2A GDP sing 108 n n PA O5' GDP sing 109 n n O2A HOA2 GDP sing 110 n n O5' C5' GDP sing 111 n n C5' C4' GDP sing 112 n n C5' H5' GDP sing 113 n n C5' "H5''" GDP sing 114 n n C4' O4' GDP sing 115 n n C4' C3' GDP sing 116 n n C4' H4' GDP sing 117 n n O4' C1' GDP sing 118 n n C3' O3' GDP sing 119 n n C3' C2' GDP sing 120 n n C3' H3' GDP sing 121 n n O3' HO3' GDP sing 122 n n C2' O2' GDP sing 123 n n C2' C1' GDP sing 124 n n C2' H2' GDP sing 125 n n O2' HO2' GDP sing 126 n n C1' N9 GDP sing 127 n n C1' H1' GDP sing 128 n n N9 C8 GDP sing 129 n y N9 C4 GDP sing 130 n y C8 N7 GDP doub 131 n y C8 H8 GDP sing 132 n n N7 C5 GDP sing 133 n y C5 C6 GDP sing 134 n n C5 C4 GDP doub 135 n y C6 O6 GDP doub 136 n n C6 N1 GDP sing 137 n n N1 C2 GDP sing 138 n n N1 HN1 GDP sing 139 n n C2 N2 GDP sing 140 n n C2 N3 GDP doub 141 n n N2 HN21 GDP sing 142 n n N2 HN22 GDP sing 143 n n N3 C4 GDP sing 144 n n # _atom_sites.entry_id 5GOM _atom_sites.fract_transf_matrix[1][1] 0.006844 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000267 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021748 _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] 0.006846 _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 C 2 GDP A 1 901 901 GDP GDP . D 3 DTT A 1 902 902 DTT DTT . E 2 GDP B 1 901 901 GDP GDP . F 4 HOH A 1 1001 1001 HOH HOH . G 4 HOH B 1 1001 1001 HOH HOH . G 4 HOH B 2 1002 1003 HOH HOH . G 4 HOH B 3 1003 1002 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 . . . E 2 -33.464 22.341 37.762 1 70.68 ? PB GDP 901 B 1 HETATM 2 O O1B GDP . . . E 2 -32.991 23.049 36.516 1 72.5 ? O1B GDP 901 B 1 HETATM 3 O O2B GDP . . . E 2 -34.935 22.631 37.98 1 75.67 ? O2B GDP 901 B 1 HETATM 4 O O3B GDP . . . E 2 -32.634 22.768 38.956 1 66.82 ? O3B GDP 901 B 1 HETATM 5 O O3A GDP . . . E 2 -33.339 20.758 37.588 1 64.92 ? O3A GDP 901 B 1 HETATM 6 P PA GDP . . . E 2 -33.955 20.062 36.28 1 64.81 ? PA GDP 901 B 1 HETATM 7 O O1A GDP . . . E 2 -34.529 21.097 35.349 1 69.2 ? O1A GDP 901 B 1 HETATM 8 O O2A GDP . . . E 2 -34.924 18.954 36.615 1 55.84 ? O2A GDP 901 B 1 HETATM 9 O O5' GDP . . . E 2 -32.672 19.349 35.64 1 74.12 ? O5' GDP 901 B 1 HETATM 10 C C5' GDP . . . E 2 -32.171 19.744 34.371 1 69.85 ? C5' GDP 901 B 1 HETATM 11 C C4' GDP . . . E 2 -31.862 18.472 33.619 1 61.1 ? C4' GDP 901 B 1 HETATM 12 O O4' GDP . . . E 2 -31.386 17.486 34.536 1 55.23 ? O4' GDP 901 B 1 HETATM 13 C C3' GDP . . . E 2 -33.154 17.934 33.05 1 60.86 ? C3' GDP 901 B 1 HETATM 14 O O3' GDP . . . E 2 -33.07 17.882 31.621 1 70.86 ? O3' GDP 901 B 1 HETATM 15 C C2' GDP . . . E 2 -33.305 16.552 33.649 1 55.48 ? C2' GDP 901 B 1 HETATM 16 O O2' GDP . . . E 2 -33.766 15.609 32.683 1 59.44 ? O2' GDP 901 B 1 HETATM 17 C C1' GDP . . . E 2 -31.914 16.228 34.149 1 52.25 ? C1' GDP 901 B 1 HETATM 18 N N9 GDP . . . E 2 -31.955 15.333 35.308 1 63.1 ? N9 GDP 901 B 1 HETATM 19 C C8 GDP . . . E 2 -32.588 15.587 36.466 1 67.03 ? C8 GDP 901 B 1 HETATM 20 N N7 GDP . . . E 2 -32.431 14.547 37.334 1 71.05 ? N7 GDP 901 B 1 HETATM 21 C C5 GDP . . . E 2 -31.675 13.615 36.729 1 71.34 ? C5 GDP 901 B 1 HETATM 22 C C6 GDP . . . E 2 -31.123 12.286 37.08 1 69.78 ? C6 GDP 901 B 1 HETATM 23 O O6 GDP . . . E 2 -31.341 11.77 38.189 1 69.28 ? O6 GDP 901 B 1 HETATM 24 N N1 GDP . . . E 2 -30.384 11.649 36.161 1 71.57 ? N1 GDP 901 B 1 HETATM 25 C C2 GDP . . . E 2 -30.127 12.168 34.943 1 63.24 ? C2 GDP 901 B 1 HETATM 26 N N2 GDP . . . E 2 -29.384 11.437 34.088 1 53.5 ? N2 GDP 901 B 1 HETATM 27 N N3 GDP . . . E 2 -30.587 13.383 34.556 1 66.77 ? N3 GDP 901 B 1 HETATM 28 C C4 GDP . . . E 2 -31.357 14.14 35.386 1 71.09 ? C4 GDP 901 B 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #