data_6HJH # _model_server_result.job_id Q2djXa3WvyCYrEwaHGEASg _model_server_result.datetime_utc '2024-11-16 06:46:24' _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 6hjh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":200}' # _entry.id 6HJH # _exptl.entry_id 6HJH _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 90 _cell.angle_gamma 120 _cell.entry_id 6HJH _cell.length_a 73.55 _cell.length_b 73.55 _cell.length_c 97.09 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6HJH _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 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 6HJH _atom_sites.fract_transf_matrix[1][1] 0.013596 _atom_sites.fract_transf_matrix[1][2] 0.00785 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.0157 _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] 0.0103 _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 1 200 200 GDP GDP . C 3 HOH A 1 301 2 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 31.077 -15.719 6.84 1 84.59 ? PB GDP 200 A 1 HETATM 2 O O1B GDP . . . B 2 31.266 -15.445 5.353 1 84.51 ? O1B GDP 200 A 1 HETATM 3 O O2B GDP . . . B 2 31.095 -17.237 7.007 1 84.79 ? O2B GDP 200 A 1 HETATM 4 O O3B GDP . . . B 2 32.095 -15.029 7.694 1 84.41 ? O3B GDP 200 A 1 HETATM 5 O O3A GDP . . . B 2 29.602 -15.236 7.204 1 83.82 ? O3A GDP 200 A 1 HETATM 6 P PA GDP . . . B 2 28.981 -13.862 7.724 1 82.3 ? PA GDP 200 A 1 HETATM 7 O O1A GDP . . . B 2 27.611 -13.705 7.181 1 81.89 ? O1A GDP 200 A 1 HETATM 8 O O2A GDP . . . B 2 29.863 -12.715 7.244 1 81.46 ? O2A GDP 200 A 1 HETATM 9 O O5' GDP . . . B 2 29.01 -13.841 9.325 1 81.91 ? O5' GDP 200 A 1 HETATM 10 C C5' GDP . . . B 2 28.221 -14.764 10.107 1 81.91 ? C5' GDP 200 A 1 HETATM 11 C C4' GDP . . . B 2 27.34 -14.03 11.093 1 80.85 ? C4' GDP 200 A 1 HETATM 12 O O4' GDP . . . B 2 28.124 -13.082 11.851 1 80.25 ? O4' GDP 200 A 1 HETATM 13 C C3' GDP . . . B 2 26.156 -13.251 10.517 1 80.03 ? C3' GDP 200 A 1 HETATM 14 O O3' GDP . . . B 2 24.998 -13.417 11.331 1 79.63 ? O3' GDP 200 A 1 HETATM 15 C C2' GDP . . . B 2 26.656 -11.806 10.538 1 79.64 ? C2' GDP 200 A 1 HETATM 16 O O2' GDP . . . B 2 25.605 -10.855 10.647 1 79.72 ? O2' GDP 200 A 1 HETATM 17 C C1' GDP . . . B 2 27.501 -11.816 11.805 1 79.71 ? C1' GDP 200 A 1 HETATM 18 N N9 GDP . . . B 2 28.539 -10.783 11.85 1 79.61 ? N9 GDP 200 A 1 HETATM 19 C C8 GDP . . . B 2 29.613 -10.625 11.015 1 80.31 ? C8 GDP 200 A 1 HETATM 20 N N7 GDP . . . B 2 30.395 -9.632 11.354 1 80.29 ? N7 GDP 200 A 1 HETATM 21 C C5 GDP . . . B 2 29.798 -9.104 12.485 1 80.38 ? C5 GDP 200 A 1 HETATM 22 C C6 GDP . . . B 2 30.196 -8.034 13.343 1 82.11 ? C6 GDP 200 A 1 HETATM 23 O O6 GDP . . . B 2 31.171 -7.297 13.208 1 83.12 ? O6 GDP 200 A 1 HETATM 24 N N1 GDP . . . B 2 29.321 -7.86 14.401 1 82.45 ? N1 GDP 200 A 1 HETATM 25 C C2 GDP . . . B 2 28.192 -8.606 14.623 1 81.75 ? C2 GDP 200 A 1 HETATM 26 N N2 GDP . . . B 2 27.464 -8.301 15.698 1 82.74 ? N2 GDP 200 A 1 HETATM 27 N N3 GDP . . . B 2 27.806 -9.601 13.83 1 79.92 ? N3 GDP 200 A 1 HETATM 28 C C4 GDP . . . B 2 28.648 -9.8 12.795 1 79.54 ? C4 GDP 200 A 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #