data_5OGK # _model_server_result.job_id 1ge9xzMNrfHZjqpbNwRCrA _model_server_result.datetime_utc '2025-03-06 20:53:09' _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 5ogk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":401}' # _entry.id 5OGK # _exptl.entry_id 5OGK _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 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 89.86 _cell.angle_beta 90.07 _cell.angle_gamma 90.11 _cell.entry_id 5OGK _cell.length_a 45.319 _cell.length_b 101.694 _cell.length_c 180.192 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5OGK _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 software_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 PISA dimeric 2 software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,I,J,K 1 1 C,E,L,M,P,Q 2 1 D,N,O 3 1 F 3 2 G,R,S 4 1 H 4 3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 1_554 x,y,z-1 1 0 0 0 1 0 0 0 1 0.220146 -0.43987 -180.191329 3 'crystal symmetry operation' 1_556 x,y,z+1 1 0 0 0 1 0 0 0 1 -0.220146 0.43987 180.191329 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 I N N ? 2 N N N ? 2 P 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 5OGK _atom_sites.fract_transf_matrix[1][1] 0.022066 _atom_sites.fract_transf_matrix[1][2] 0.000044 _atom_sites.fract_transf_matrix[1][3] 0.000028 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009833 _atom_sites.fract_transf_matrix[2][3] -0.000024 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.00555 _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 I 2 GDD A 1 401 1 GDD GDD . J 3 OLC A 1 402 1 OLC OLC . K 3 OLC A 1 403 4 OLC OLC . L 3 OLC C 1 401 5 OLC OLC . M 3 OLC C 1 402 8 OLC OLC . N 2 GDD D 1 401 1 GDD GDD . O 3 OLC D 1 402 7 OLC OLC . P 2 GDD E 1 401 1 GDD GDD . Q 3 OLC E 1 402 6 OLC OLC . R 3 OLC G 1 401 2 OLC OLC . S 3 OLC G 1 402 3 OLC OLC . # 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 . . . I 2 4.651 20.531 25.473 0.9 88.91 ? N2 GDD 401 A 1 HETATM 2 C C2 GDD . . . I 2 5.223 21.737 25.457 0.9 99.32 ? C2 GDD 401 A 1 HETATM 3 N N1 GDD . . . I 2 5.957 22.061 24.346 0.9 98.8 ? N1 GDD 401 A 1 HETATM 4 N N3 GDD . . . I 2 5.061 22.555 26.494 0.9 103.68 ? N3 GDD 401 A 1 HETATM 5 C C4 GDD . . . I 2 5.696 23.733 26.334 0.9 107.27 ? C4 GDD 401 A 1 HETATM 6 C C5 GDD . . . I 2 6.457 24.152 25.263 0.9 105.93 ? C5 GDD 401 A 1 HETATM 7 C C6 GDD . . . I 2 6.619 23.258 24.151 0.9 101.49 ? C6 GDD 401 A 1 HETATM 8 O O6 GDD . . . I 2 7.251 23.461 23.115 0.9 103.8 ? O6 GDD 401 A 1 HETATM 9 N N7 GDD . . . I 2 6.94 25.432 25.483 0.9 104.39 ? N7 GDD 401 A 1 HETATM 10 C C8 GDD . . . I 2 6.468 25.76 26.665 0.9 107.11 ? C8 GDD 401 A 1 HETATM 11 N N9 GDD . . . I 2 5.703 24.773 27.234 0.9 111.5 ? N9 GDD 401 A 1 HETATM 12 C C1' GDD . . . I 2 5.007 24.806 28.535 0.9 109.74 ? C1' GDD 401 A 1 HETATM 13 C C2' GDD . . . I 2 5.928 24.925 29.743 0.9 111.55 ? C2' GDD 401 A 1 HETATM 14 O O2' GDD . . . I 2 6.466 23.659 30.109 0.9 103.33 ? O2' GDD 401 A 1 HETATM 15 C C3' GDD . . . I 2 4.946 25.46 30.79 0.9 114.74 ? C3' GDD 401 A 1 HETATM 16 O O3' GDD . . . I 2 4.219 24.412 31.422 0.9 112.97 ? O3' GDD 401 A 1 HETATM 17 C C4' GDD . . . I 2 4.002 26.342 29.963 0.9 114.6 ? C4' GDD 401 A 1 HETATM 18 O O4' GDD . . . I 2 4.19 25.958 28.58 0.9 109.33 ? O4' GDD 401 A 1 HETATM 19 C C5' GDD . . . I 2 4.211 27.828 30.118 0.9 116.51 ? C5' GDD 401 A 1 HETATM 20 O O5' GDD . . . I 2 5.621 28.082 30.292 0.9 125.45 ? O5' GDD 401 A 1 HETATM 21 P PA GDD . . . I 2 6.269 28.678 31.656 0.9 140.34 ? PA GDD 401 A 1 HETATM 22 O O1A GDD . . . I 2 6.391 30.15 31.551 0.9 130.87 ? O1A GDD 401 A 1 HETATM 23 O O2A GDD . . . I 2 7.611 27.954 31.825 0.9 124.64 ? O2A GDD 401 A 1 HETATM 24 O O3A GDD . . . I 2 5.349 28.255 32.889 0.9 125.78 ? O3A GDD 401 A 1 HETATM 25 P PB GDD . . . I 2 5.622 27.582 34.31 0.9 131.6 ? PB GDD 401 A 1 HETATM 26 O O2B GDD . . . I 2 5.1 26.148 34.221 0.9 117.15 ? O2B GDD 401 A 1 HETATM 27 O O3B GDD . . . I 2 7.053 27.685 34.681 0.9 109.53 ? O3B GDD 401 A 1 HETATM 28 O O1B GDD . . . I 2 4.701 28.345 35.438 0.9 114.66 ? O1B GDD 401 A 1 HETATM 29 C C11 GDD . . . I 2 3.3 28.432 35.521 0.9 100.86 ? C11 GDD 401 A 1 HETATM 30 O O51 GDD . . . I 2 2.866 28.298 36.863 0.9 87.96 ? O51 GDD 401 A 1 HETATM 31 C C51 GDD . . . I 2 3.447 29.268 37.751 0.9 86.81 ? C51 GDD 401 A 1 HETATM 32 C C61 GDD . . . I 2 2.934 28.952 39.138 0.9 80.61 ? C61 GDD 401 A 1 HETATM 33 O O6A GDD . . . I 2 3.344 27.663 39.572 0.9 78.84 ? O6A GDD 401 A 1 HETATM 34 C C21 GDD . . . I 2 2.868 29.785 34.974 0.9 96.87 ? C21 GDD 401 A 1 HETATM 35 O O21 GDD . . . I 2 1.447 29.877 34.977 0.9 77.7 ? O21 GDD 401 A 1 HETATM 36 C C31 GDD . . . I 2 3.464 30.889 35.837 0.9 99.21 ? C31 GDD 401 A 1 HETATM 37 O O31 GDD . . . I 2 3.014 32.162 35.387 0.9 89.01 ? O31 GDD 401 A 1 HETATM 38 C C41 GDD . . . I 2 3.093 30.683 37.301 0.9 91.57 ? C41 GDD 401 A 1 HETATM 39 O O41 GDD . . . I 2 3.805 31.61 38.115 0.9 84.6 ? O41 GDD 401 A 1 HETATM 40 H H2N1 GDD . . . I 2 4.095 20.236 26.27 0.9 106.9 ? H2N1 GDD 401 A 1 HETATM 41 H H2N2 GDD . . . I 2 4.733 19.857 24.718 0.9 106.9 ? H2N2 GDD 401 A 1 HETATM 42 H H1 GDD . . . I 2 6.044 21.395 23.585 0.9 118.76 ? H1 GDD 401 A 1 HETATM 43 H H8 GDD . . . I 2 6.661 26.717 27.147 0.9 128.74 ? H8 GDD 401 A 1 HETATM 44 H H1' GDD . . . I 2 4.356 23.935 28.592 0.9 131.9 ? H1' GDD 401 A 1 HETATM 45 H H2' GDD . . . I 2 6.732 25.638 29.562 0.9 134.07 ? H2' GDD 401 A 1 HETATM 46 H HA GDD . . . I 2 7.235 23.505 29.5 0.9 124.2 ? HA GDD 401 A 1 HETATM 47 H H3' GDD . . . I 2 5.457 26.038 31.559 0.9 137.9 ? H3' GDD 401 A 1 HETATM 48 H HB GDD . . . I 2 3.693 23.97 30.706 0.9 135.77 ? HB GDD 401 A 1 HETATM 49 H H4' GDD . . . I 2 2.969 26.067 30.171 0.9 137.73 ? H4' GDD 401 A 1 HETATM 50 H "H5'1" GDD . . . I 2 3.841 28.4 29.268 0.9 140.02 ? "H5'1" GDD 401 A 1 HETATM 51 H "H5'2" GDD . . . I 2 3.76 28.247 31.016 0.9 140.02 ? "H5'2" GDD 401 A 1 HETATM 52 H HO2A GDD . . . I 2 7.896 27.064 31.489 0.9 149.77 ? HO2A GDD 401 A 1 HETATM 53 H HO2B GDD . . . I 2 4.219 25.752 33.991 0.9 140.79 ? HO2B GDD 401 A 1 HETATM 54 H H11 GDD . . . I 2 2.834 27.576 35.034 0.9 121.24 ? H11 GDD 401 A 1 HETATM 55 H H51 GDD . . . I 2 4.528 29.135 37.747 0.9 104.38 ? H51 GDD 401 A 1 HETATM 56 H H611 GDD . . . I 2 3.306 29.72 39.815 0.9 96.94 ? H611 GDD 401 A 1 HETATM 57 H H612 GDD . . . I 2 1.849 29.031 39.177 0.9 96.94 ? H612 GDD 401 A 1 HETATM 58 H H6A GDD . . . I 2 2.733 27.434 40.321 0.9 94.81 ? H6A GDD 401 A 1 HETATM 59 H H21 GDD . . . I 2 3.189 29.906 33.94 0.9 116.46 ? H21 GDD 401 A 1 HETATM 60 H HC GDD . . . I 2 1.152 30.295 34.126 0.9 93.45 ? HC GDD 401 A 1 HETATM 61 H H31 GDD . . . I 2 4.545 30.926 35.712 0.9 119.26 ? H31 GDD 401 A 1 HETATM 62 H HD GDD . . . I 2 2.141 32.093 34.918 0.9 107.01 ? HD GDD 401 A 1 HETATM 63 H H41 GDD . . . I 2 2.02 30.833 37.418 0.9 110.09 ? H41 GDD 401 A 1 HETATM 64 H HE GDD . . . I 2 3.494 32.515 37.853 0.9 101.73 ? HE GDD 401 A 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 64 #