data_7WHT # _model_server_result.job_id kQICsJ7RuKs0FNKFqHs4yQ _model_server_result.datetime_utc '2024-10-20 01:35:30' _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 7wht # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":601}' # _entry.id 7WHT # _exptl.entry_id 7WHT _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 605.341 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE" _entity.pdbx_number_of_molecules 6 _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 7WHT _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7WHT _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,H,I,J,K,L,M,N,O,P,Q,R _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 ? _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 G N N ? 2 I N N ? 2 K N N ? 2 M N N ? 2 O N N ? 2 Q 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 OD2 ASP 118 A ASP 118 1_555 H MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc2 A OD1 ASP 226 A ASP 226 1_555 H MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.518 ? metalc ? metalc3 G O2A GDD . A GDD 601 1_555 H MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc4 G O3A GDD . A GDD 601 1_555 H MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? metalc ? metalc5 B OD1 ASP 118 B ASP 118 1_555 J MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.718 ? metalc ? metalc6 B OD2 ASP 118 B ASP 118 1_555 J MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc7 B OD1 ASP 226 B ASP 226 1_555 J MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? metalc ? metalc8 B OD2 ASP 226 B ASP 226 1_555 J MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.798 ? metalc ? metalc9 I O2A GDD . B GDD 601 1_555 J MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc10 C OD2 ASP 118 C ASP 118 1_555 L MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc11 C OD1 ASP 226 C ASP 226 1_555 L MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.574 ? metalc ? metalc12 K O2A GDD . C GDD 601 1_555 L MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc13 K O3A GDD . C GDD 601 1_555 L MG MG . C MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc14 D OD2 ASP 118 D ASP 118 1_555 N MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc15 D OD1 ASP 226 D ASP 226 1_555 N MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? metalc ? metalc16 M O2A GDD . D GDD 601 1_555 N MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc17 M O3A GDD . D GDD 601 1_555 N MG MG . D MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.457 ? metalc ? metalc18 E OD2 ASP 118 E ASP 118 1_555 P MG MG . E MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc19 E OD1 ASP 226 E ASP 226 1_555 P MG MG . E MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.696 ? metalc ? metalc20 E OD2 ASP 226 E ASP 226 1_555 P MG MG . E MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.792 ? metalc ? metalc21 O O2A GDD . E GDD 601 1_555 P MG MG . E MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc22 O O3A GDD . E GDD 601 1_555 P MG MG . E MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.771 ? metalc ? metalc23 F OD2 ASP 118 F ASP 118 1_555 R MG MG . F MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc24 F OD1 ASP 226 F ASP 226 1_555 R MG MG . F MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.531 ? metalc ? metalc25 Q O2A GDD . F GDD 601 1_555 R MG MG . F MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? metalc ? metalc26 Q O3A GDD . F GDD 601 1_555 R MG MG . F MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? # _chem_comp.formula 'C16 H25 N5 O16 P2' _chem_comp.formula_weight 605.341 _chem_comp.id GDD _chem_comp.mon_nstd_flag . _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE-ALPHA-D-MANNOSE" _chem_comp.type non-polymer _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 N2 C2 GDD sing 83 n n N2 H2N1 GDD sing 84 n n N2 H2N2 GDD sing 85 n n C2 N1 GDD sing 86 n n C2 N3 GDD doub 87 n n N1 C6 GDD sing 88 n n N1 H1 GDD sing 89 n n N3 C4 GDD sing 90 n n C4 C5 GDD doub 91 n y C4 N9 GDD sing 92 n y C5 C6 GDD sing 93 n n C5 N7 GDD sing 94 n y C6 O6 GDD doub 95 n n N7 C8 GDD doub 96 n y C8 N9 GDD sing 97 n y C8 H8 GDD sing 98 n n N9 C1' GDD sing 99 n n C1' C2' GDD sing 100 n n C1' O4' GDD sing 101 n n C1' H1' GDD sing 102 n n C2' O2' GDD sing 103 n n C2' C3' GDD sing 104 n n C2' H2' GDD sing 105 n n O2' HA GDD sing 106 n n C3' O3' GDD sing 107 n n C3' C4' GDD sing 108 n n C3' H3' GDD sing 109 n n O3' HB GDD sing 110 n n C4' O4' GDD sing 111 n n C4' C5' GDD sing 112 n n C4' H4' GDD sing 113 n n C5' O5' GDD sing 114 n n C5' "H5'1" GDD sing 115 n n C5' "H5'2" GDD sing 116 n n O5' PA GDD sing 117 n n PA O1A GDD doub 118 n n PA O2A GDD sing 119 n n PA O3A GDD sing 120 n n O2A HO2A GDD sing 121 n n O3A PB GDD sing 122 n n PB O2B GDD sing 123 n n PB O3B GDD doub 124 n n PB O1B GDD sing 125 n n O2B HO2B GDD sing 126 n n O1B C11 GDD sing 127 n n C11 O51 GDD sing 128 n n C11 C21 GDD sing 129 n n C11 H11 GDD sing 130 n n O51 C51 GDD sing 131 n n C51 C61 GDD sing 132 n n C51 C41 GDD sing 133 n n C51 H51 GDD sing 134 n n C61 O6A GDD sing 135 n n C61 H611 GDD sing 136 n n C61 H612 GDD sing 137 n n O6A H6A GDD sing 138 n n C21 O21 GDD sing 139 n n C21 C31 GDD sing 140 n n C21 H21 GDD sing 141 n n O21 HC GDD sing 142 n n C31 O31 GDD sing 143 n n C31 C41 GDD sing 144 n n C31 H31 GDD sing 145 n n O31 HD GDD sing 146 n n C41 O41 GDD sing 147 n n C41 H41 GDD sing 148 n n O41 HE GDD sing 149 n n # _atom_sites.entry_id 7WHT _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 G 2 GDD A 1 601 601 GDD GDD . H 3 MG A 1 602 1 MG MG . I 2 GDD B 1 601 601 GDD GDD . J 3 MG B 1 602 2 MG MG . K 2 GDD C 1 601 601 GDD GDD . L 3 MG C 1 602 3 MG MG . M 2 GDD D 1 601 601 GDD GDD . N 3 MG D 1 602 4 MG MG . O 2 GDD E 1 601 601 GDD GDD . P 3 MG E 1 602 5 MG MG . Q 2 GDD F 1 601 601 GDD GDD . R 3 MG F 1 602 6 MG MG . # 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 N N2 GDD . . . G 2 110.265 119.562 121.959 1 104.11 ? N2 GDD 601 A 1 HETATM 2 C C2 GDD . . . G 2 108.981 119.394 121.561 1 104.11 ? C2 GDD 601 A 1 HETATM 3 N N1 GDD . . . G 2 107.972 119.669 122.388 1 104.11 ? N1 GDD 601 A 1 HETATM 4 N N3 GDD . . . G 2 108.753 118.945 120.315 1 104.11 ? N3 GDD 601 A 1 HETATM 5 C C4 GDD . . . G 2 107.504 118.747 119.828 1 104.11 ? C4 GDD 601 A 1 HETATM 6 C C5 GDD . . . G 2 106.379 119.034 120.694 1 104.11 ? C5 GDD 601 A 1 HETATM 7 C C6 GDD . . . G 2 106.699 119.519 122.032 1 104.11 ? C6 GDD 601 A 1 HETATM 8 O O6 GDD . . . G 2 105.786 119.777 122.811 1 104.11 ? O6 GDD 601 A 1 HETATM 9 N N7 GDD . . . G 2 105.271 118.768 120.011 1 104.11 ? N7 GDD 601 A 1 HETATM 10 C C8 GDD . . . G 2 105.658 118.342 118.796 1 104.11 ? C8 GDD 601 A 1 HETATM 11 N N9 GDD . . . G 2 106.963 118.335 118.706 1 104.11 ? N9 GDD 601 A 1 HETATM 12 C C1' GDD . . . G 2 107.642 117.924 117.522 1 104.11 ? C1' GDD 601 A 1 HETATM 13 C C2' GDD . . . G 2 107.642 119.052 116.587 1 104.11 ? C2' GDD 601 A 1 HETATM 14 O O2' GDD . . . G 2 106.471 118.766 115.869 1 104.11 ? O2' GDD 601 A 1 HETATM 15 C C3' GDD . . . G 2 108.854 118.756 115.762 1 104.11 ? C3' GDD 601 A 1 HETATM 16 O O3' GDD . . . G 2 108.477 118.006 114.61 1 104.11 ? O3' GDD 601 A 1 HETATM 17 C C4' GDD . . . G 2 109.685 117.856 116.63 1 104.11 ? C4' GDD 601 A 1 HETATM 18 O O4' GDD . . . G 2 108.975 117.628 117.812 1 104.11 ? O4' GDD 601 A 1 HETATM 19 C C5' GDD . . . G 2 111.081 118.356 116.909 1 104.11 ? C5' GDD 601 A 1 HETATM 20 O O5' GDD . . . G 2 111.101 119.198 118.037 1 104.11 ? O5' GDD 601 A 1 HETATM 21 P PA GDD . . . G 2 111.28 120.739 117.757 1 104.11 ? PA GDD 601 A 1 HETATM 22 O O1A GDD . . . G 2 112.313 121.303 118.671 1 104.11 ? O1A GDD 601 A 1 HETATM 23 O O2A GDD . . . G 2 109.89 121.249 117.718 1 104.11 ? O2A GDD 601 A 1 HETATM 24 O O3A GDD . . . G 2 111.849 120.758 116.292 1 104.11 ? O3A GDD 601 A 1 HETATM 25 P PB GDD . . . G 2 113.413 120.91 116.084 1 104.11 ? PB GDD 601 A 1 HETATM 26 O O2B GDD . . . G 2 114.071 119.724 116.709 1 104.11 ? O2B GDD 601 A 1 HETATM 27 O O3B GDD . . . G 2 113.863 122.287 116.454 1 104.11 ? O3B GDD 601 A 1 HETATM 28 O O1B GDD . . . G 2 113.453 120.732 114.506 1 104.11 ? O1B GDD 601 A 1 HETATM 29 C C11 GDD . . . G 2 112.353 120.075 113.907 1 104.11 ? C11 GDD 601 A 1 HETATM 30 O O51 GDD . . . G 2 111.366 121.04 113.536 1 104.11 ? O51 GDD 601 A 1 HETATM 31 C C51 GDD . . . G 2 111.685 121.771 112.37 1 104.11 ? C51 GDD 601 A 1 HETATM 32 C C61 GDD . . . G 2 110.611 122.804 112.141 1 104.11 ? C61 GDD 601 A 1 HETATM 33 O O6A GDD . . . G 2 111.225 124.062 112.35 1 104.11 ? O6A GDD 601 A 1 HETATM 34 C C21 GDD . . . G 2 112.854 119.302 112.703 1 104.11 ? C21 GDD 601 A 1 HETATM 35 O O21 GDD . . . G 2 113.075 117.938 113.03 1 104.11 ? O21 GDD 601 A 1 HETATM 36 C C31 GDD . . . G 2 111.769 119.365 111.68 1 104.11 ? C31 GDD 601 A 1 HETATM 37 O O31 GDD . . . G 2 110.57 119.001 112.35 1 104.11 ? O31 GDD 601 A 1 HETATM 38 C C41 GDD . . . G 2 111.717 120.795 111.221 1 104.11 ? C41 GDD 601 A 1 HETATM 39 O O41 GDD . . . G 2 112.907 121.013 110.478 1 104.11 ? O41 GDD 601 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 39 #