data_3LX8 # _model_server_result.job_id 9rAnJF2jxz-ietzdW38_8A _model_server_result.datetime_utc '2024-11-18 10:32:27' _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 3lx8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":300}' # _entry.id 3LX8 # _exptl.entry_id 3LX8 _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 90 _cell.entry_id 3LX8 _cell.length_a 42.8 _cell.length_b 42.8 _cell.length_c 282.1 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LX8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _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 _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 3LX8 _atom_sites.fract_transf_matrix[1][1] 0.023368 _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] 0.023368 _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] 0.003545 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id GDP _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 300 _pdbx_nonpoly_scheme.auth_seq_num 300 _pdbx_nonpoly_scheme.pdb_mon_id GDP _pdbx_nonpoly_scheme.auth_mon_id GDP _pdbx_nonpoly_scheme.pdb_ins_code . # 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 9.822 16.893 -32.528 1 47.44 ? PB GDP 300 A 1 HETATM 2 O O1B GDP . . . B 2 9.712 17.184 -31.07 1 47.81 ? O1B GDP 300 A 1 HETATM 3 O O2B GDP . . . B 2 8.357 16.81 -33.265 1 46.54 ? O2B GDP 300 A 1 HETATM 4 O O3B GDP . . . B 2 10.548 15.464 -32.831 1 46.98 ? O3B GDP 300 A 1 HETATM 5 O O3A GDP . . . B 2 10.652 18.023 -33.316 1 47.94 ? O3A GDP 300 A 1 HETATM 6 P PA GDP . . . B 2 11.824 17.625 -34.377 1 48.3 ? PA GDP 300 A 1 HETATM 7 O O1A GDP . . . B 2 12.924 16.84 -33.757 1 47.78 ? O1A GDP 300 A 1 HETATM 8 O O2A GDP . . . B 2 11.069 16.809 -35.594 1 48.2 ? O2A GDP 300 A 1 HETATM 9 O O5' GDP . . . B 2 12.315 19.005 -35.002 1 49.2 ? O5' GDP 300 A 1 HETATM 10 C C5' GDP . . . B 2 11.382 19.842 -35.719 1 50.73 ? C5' GDP 300 A 1 HETATM 11 C C4' GDP . . . B 2 12.045 21.137 -36.21 1 51.55 ? C4' GDP 300 A 1 HETATM 12 O O4' GDP . . . B 2 12.725 21.71 -35.074 1 52.08 ? O4' GDP 300 A 1 HETATM 13 C C3' GDP . . . B 2 13.104 20.825 -37.276 1 51.64 ? C3' GDP 300 A 1 HETATM 14 O O3' GDP . . . B 2 12.846 21.649 -38.425 1 51.67 ? O3' GDP 300 A 1 HETATM 15 C C2' GDP . . . B 2 14.438 21.177 -36.608 1 51.8 ? C2' GDP 300 A 1 HETATM 16 O O2' GDP . . . B 2 15.279 21.885 -37.516 1 53.4 ? O2' GDP 300 A 1 HETATM 17 C C1' GDP . . . B 2 14.033 22.132 -35.494 1 52.05 ? C1' GDP 300 A 1 HETATM 18 N N9 GDP . . . B 2 14.907 22.076 -34.279 1 52.2 ? N9 GDP 300 A 1 HETATM 19 C C8 GDP . . . B 2 14.998 21.085 -33.393 1 52.51 ? C8 GDP 300 A 1 HETATM 20 N N7 GDP . . . B 2 15.877 21.415 -32.45 1 52.76 ? N7 GDP 300 A 1 HETATM 21 C C5 GDP . . . B 2 16.354 22.621 -32.728 1 53.3 ? C5 GDP 300 A 1 HETATM 22 C C6 GDP . . . B 2 17.284 23.456 -32.105 1 54.59 ? C6 GDP 300 A 1 HETATM 23 O O6 GDP . . . B 2 17.855 23.118 -31.069 1 55.23 ? O6 GDP 300 A 1 HETATM 24 N N1 GDP . . . B 2 17.567 24.708 -32.68 1 55.42 ? N1 GDP 300 A 1 HETATM 25 C C2 GDP . . . B 2 16.9 25.079 -33.866 1 54.79 ? C2 GDP 300 A 1 HETATM 26 N N2 GDP . . . B 2 17.141 26.252 -34.439 1 56.01 ? N2 GDP 300 A 1 HETATM 27 N N3 GDP . . . B 2 16.013 24.247 -34.43 1 53.48 ? N3 GDP 300 A 1 HETATM 28 C C4 GDP . . . B 2 15.731 23.044 -33.896 1 52.75 ? C4 GDP 300 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 234 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #