data_8OUL # _model_server_result.job_id tKaeMRXbbe52QBy11BluOA _model_server_result.datetime_utc '2024-10-11 02:19:59' _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 8oul # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":201}' # _entry.id 8OUL # _exptl.entry_id 8OUL _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 3 _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 8OUL _cell.length_a 75.693 _cell.length_b 75.693 _cell.length_c 189.306 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8OUL _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,J 1 1 B,F,G,K 2 1 C,H,I,L 3 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 D N N ? 2 F N N ? 2 H N 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 A OG SER 31 A SER 31 1_555 E MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.707 ? metalc ? metalc2 D O2B GDP . A GDP 201 1_555 E MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc3 B OG SER 31 B SER 31 1_555 G MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.649 ? metalc ? metalc4 F O2B GDP . B GDP 201 1_555 G MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? metalc ? metalc5 G MG MG . B MG 202 1_555 K O HOH . B HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.656 ? metalc ? metalc6 C OG SER 31 C SER 31 1_555 I MG MG . C MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.62 ? metalc ? metalc7 C OD2 ASP 68 C ASP 68 1_555 I MG MG . C MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.996 ? metalc ? metalc8 H O2B GDP . C GDP 201 1_555 I MG MG . C MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? # _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 8OUL _atom_sites.fract_transf_matrix[1][1] 0.013211 _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] 0.013211 _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] 0.005282 _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 D 2 GDP A 1 201 200 GDP GDP . E 3 MG A 1 202 300 MG MG . F 2 GDP B 1 201 200 GDP GDP . G 3 MG B 1 202 300 MG MG . H 2 GDP C 1 201 200 GDP GDP . I 3 MG C 1 202 300 MG MG . J 4 HOH A 1 301 6 HOH HOH . K 4 HOH B 1 301 9 HOH HOH . K 4 HOH B 2 302 8 HOH HOH . K 4 HOH B 3 303 1 HOH HOH . K 4 HOH B 4 304 7 HOH HOH . K 4 HOH B 5 305 3 HOH HOH . K 4 HOH B 6 306 4 HOH HOH . L 4 HOH C 1 301 2 HOH HOH . L 4 HOH C 2 302 5 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 2 -14.869 -7.343 38.634 1 51.32 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . D 2 -14.382 -8.626 38.023 1 51.55 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . D 2 -13.822 -6.266 38.75 1 51.51 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . D 2 -16.153 -6.839 38.043 1 51.7 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . D 2 -15.3 -7.773 40.127 1 49.82 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . D 2 -14.261 -7.871 41.352 1 48.52 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . D 2 -12.868 -8.06 40.839 1 47.9 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . D 2 -14.561 -6.765 42.333 1 48.71 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . D 2 -14.612 -9.275 42.042 1 48.34 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . D 2 -15.865 -9.907 41.835 1 47.78 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . D 2 -16.381 -10.378 43.183 1 47.13 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . D 2 -16.286 -11.799 43.256 1 46.6 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . D 2 -15.579 -9.796 44.335 1 47.43 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . D 2 -16.451 -9.092 45.222 1 47.21 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . D 2 -14.938 -10.967 45.047 1 47.83 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . D 2 -15.298 -10.966 46.43 1 48.98 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . D 2 -15.487 -12.207 44.368 1 46.4 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . D 2 -14.377 -13.061 43.89 1 45.01 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . D 2 -13.445 -12.757 42.968 1 44.84 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . D 2 -12.593 -13.795 42.783 1 44.73 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . D 2 -12.978 -14.784 43.609 1 44.06 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . D 2 -12.533 -16.156 43.931 1 43.03 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . D 2 -11.55 -16.665 43.368 1 42.15 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . D 2 -13.223 -16.846 44.841 1 43.07 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . D 2 -14.294 -16.338 45.471 1 43.04 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . D 2 -14.932 -17.097 46.388 1 42.54 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . D 2 -14.762 -15.092 45.23 1 43.55 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . D 2 -14.156 -14.291 44.329 1 44.26 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #