data_3OY7 # _model_server_result.job_id OUbwGPU29WBsS17tGqB10g _model_server_result.datetime_utc '2025-02-18 09:21:56' _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 3oy7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":414}' # _entry.id 3OY7 # _exptl.entry_id 3OY7 _exptl.method 'X-RAY DIFFRACTION' # _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 2 _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 3OY7 _cell.length_a 154.248 _cell.length_b 243.189 _cell.length_c 67.402 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3OY7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 D N N # _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 3OY7 _atom_sites.fract_transf_matrix[1][1] 0.006483 _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] 0.004112 _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] 0.014836 _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 GDD A 1 414 301 GDD GDD . D 2 GDD B 1 414 301 GDD GDD . E 3 HOH A 1 415 2 HOH HOH . E 3 HOH A 2 416 4 HOH HOH . E 3 HOH A 3 417 5 HOH HOH . E 3 HOH A 4 418 6 HOH HOH . E 3 HOH A 5 419 9 HOH HOH . F 3 HOH B 1 415 1 HOH HOH . F 3 HOH B 2 416 3 HOH HOH . F 3 HOH B 3 417 7 HOH HOH . F 3 HOH B 4 418 8 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 N N2 GDD . . . C 2 -25.164 -57.136 -35.185 1 89.79 ? N2 GDD 414 A 1 HETATM 2 C C2 GDD . . . C 2 -24.576 -56.059 -34.671 1 89.66 ? C2 GDD 414 A 1 HETATM 3 N N1 GDD . . . C 2 -24.704 -54.822 -35.325 1 89.68 ? N1 GDD 414 A 1 HETATM 4 N N3 GDD . . . C 2 -23.865 -56.159 -33.532 1 89.62 ? N3 GDD 414 A 1 HETATM 5 C C4 GDD . . . C 2 -23.26 -55.083 -32.989 1 90.03 ? C4 GDD 414 A 1 HETATM 6 C C5 GDD . . . C 2 -23.354 -53.83 -33.597 1 90.2 ? C5 GDD 414 A 1 HETATM 7 C C6 GDD . . . C 2 -24.084 -53.689 -34.78 1 89.96 ? C6 GDD 414 A 1 HETATM 8 O O6 GDD . . . C 2 -24.187 -52.596 -35.34 1 89.56 ? O6 GDD 414 A 1 HETATM 9 N N7 GDD . . . C 2 -22.666 -52.972 -32.845 1 90.05 ? N7 GDD 414 A 1 HETATM 10 C C8 GDD . . . C 2 -22.161 -53.644 -31.811 1 90.04 ? C8 GDD 414 A 1 HETATM 11 N N9 GDD . . . C 2 -22.518 -54.93 -31.894 1 89.99 ? N9 GDD 414 A 1 HETATM 12 C C1' GDD . . . C 2 -22.157 -56.019 -30.932 1 90.02 ? C1' GDD 414 A 1 HETATM 13 C C2' GDD . . . C 2 -20.641 -56.157 -30.783 1 90.02 ? C2' GDD 414 A 1 HETATM 14 O O2' GDD . . . C 2 -20.137 -57.029 -31.803 1 90.25 ? O2' GDD 414 A 1 HETATM 15 C C3' GDD . . . C 2 -20.486 -56.776 -29.383 1 89.87 ? C3' GDD 414 A 1 HETATM 16 O O3' GDD . . . C 2 -20.034 -58.133 -29.47 1 89.45 ? O3' GDD 414 A 1 HETATM 17 C C4' GDD . . . C 2 -21.913 -56.755 -28.812 1 89.55 ? C4' GDD 414 A 1 HETATM 18 O O4' GDD . . . C 2 -22.577 -55.732 -29.583 1 90.14 ? O4' GDD 414 A 1 HETATM 19 C C5' GDD . . . C 2 -21.952 -56.492 -27.279 1 88.97 ? C5' GDD 414 A 1 HETATM 20 O O5' GDD . . . C 2 -21.514 -55.182 -26.876 1 88.5 ? O5' GDD 414 A 1 HETATM 21 P PA GDD . . . C 2 -20.775 -54.94 -25.423 1 88.03 ? PA GDD 414 A 1 HETATM 22 O O1A GDD . . . C 2 -19.407 -54.408 -25.605 1 88.22 ? O1A GDD 414 A 1 HETATM 23 O O2A GDD . . . C 2 -20.722 -56.36 -24.674 1 87.77 ? O2A GDD 414 A 1 HETATM 24 O O3A GDD . . . C 2 -21.697 -53.937 -24.509 1 87.63 ? O3A GDD 414 A 1 HETATM 25 P PB GDD . . . C 2 -23.212 -54.287 -24.011 1 86.51 ? PB GDD 414 A 1 HETATM 26 O O2B GDD . . . C 2 -24.121 -53.079 -24.592 1 86.87 ? O2B GDD 414 A 1 HETATM 27 O O3B GDD . . . C 2 -23.689 -55.599 -24.509 1 86.99 ? O3B GDD 414 A 1 HETATM 28 O O1B GDD . . . C 2 -23.231 -54.119 -22.4 1 87.41 ? O1B GDD 414 A 1 HETATM 29 C C11 GDD . . . C 2 -23.239 -55.217 -21.408 1 87.94 ? C11 GDD 414 A 1 HETATM 30 O O51 GDD . . . C 2 -23.592 -56.561 -21.908 1 88.35 ? O51 GDD 414 A 1 HETATM 31 C C51 GDD . . . C 2 -22.556 -57.613 -22.091 1 88.29 ? C51 GDD 414 A 1 HETATM 32 C C61 GDD . . . C 2 -23.129 -58.9 -21.477 1 88.3 ? C61 GDD 414 A 1 HETATM 33 O O6A GDD . . . C 2 -22.821 -60.019 -22.311 1 88.02 ? O6A GDD 414 A 1 HETATM 34 C C21 GDD . . . C 2 -21.911 -55.164 -20.63 1 87.88 ? C21 GDD 414 A 1 HETATM 35 O O21 GDD . . . C 2 -22.096 -55.751 -19.342 1 88.11 ? O21 GDD 414 A 1 HETATM 36 C C31 GDD . . . C 2 -20.807 -55.898 -21.386 1 88.01 ? C31 GDD 414 A 1 HETATM 37 O O31 GDD . . . C 2 -19.56 -55.721 -20.716 1 87.76 ? O31 GDD 414 A 1 HETATM 38 C C41 GDD . . . C 2 -21.14 -57.387 -21.506 1 88.17 ? C41 GDD 414 A 1 HETATM 39 O O41 GDD . . . C 2 -20.159 -58.009 -22.338 1 88.46 ? O41 GDD 414 A 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 239 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 39 #