data_5OGK # _model_server_result.job_id 6TA85RODojTc71KFBp0FrQ _model_server_result.datetime_utc '2025-03-06 21:34:00' _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":"P","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 . . . P 2 22.053 -33.064 9.696 0.9 93.62 ? N2 GDD 401 E 1 HETATM 2 C C2 GDD . . . P 2 22.25 -31.767 9.45 0.9 102.19 ? C2 GDD 401 E 1 HETATM 3 N N1 GDD . . . P 2 22.74 -31.434 8.215 0.9 96.26 ? N1 GDD 401 E 1 HETATM 4 N N3 GDD . . . P 2 21.949 -30.869 10.385 0.9 105.41 ? N3 GDD 401 E 1 HETATM 5 C C4 GDD . . . P 2 22.169 -29.603 9.983 0.9 108.17 ? C4 GDD 401 E 1 HETATM 6 C C5 GDD . . . P 2 22.655 -29.166 8.769 0.9 109.07 ? C5 GDD 401 E 1 HETATM 7 C C6 GDD . . . P 2 22.981 -30.147 7.774 0.9 101.98 ? C6 GDD 401 E 1 HETATM 8 O O6 GDD . . . P 2 23.426 -29.942 6.645 0.9 103.11 ? O6 GDD 401 E 1 HETATM 9 N N7 GDD . . . P 2 22.732 -27.782 8.748 0.9 114.53 ? N7 GDD 401 E 1 HETATM 10 C C8 GDD . . . P 2 22.296 -27.415 9.932 0.9 112.13 ? C8 GDD 401 E 1 HETATM 11 N N9 GDD . . . P 2 21.938 -28.472 10.728 0.9 108.69 ? N9 GDD 401 E 1 HETATM 12 C C1' GDD . . . P 2 21.41 -28.438 12.099 0.9 115.97 ? C1' GDD 401 E 1 HETATM 13 C C2' GDD . . . P 2 22.492 -28.359 13.175 0.9 118.5 ? C2' GDD 401 E 1 HETATM 14 O O2' GDD . . . P 2 22.965 -29.659 13.508 0.9 108.44 ? O2' GDD 401 E 1 HETATM 15 C C3' GDD . . . P 2 21.698 -27.715 14.309 0.9 126.41 ? C3' GDD 401 E 1 HETATM 16 O O3' GDD . . . P 2 20.881 -28.669 14.978 0.9 125.58 ? O3' GDD 401 E 1 HETATM 17 C C4' GDD . . . P 2 20.843 -26.695 13.557 0.9 125.82 ? C4' GDD 401 E 1 HETATM 18 O O4' GDD . . . P 2 20.614 -27.275 12.251 0.9 121.44 ? O4' GDD 401 E 1 HETATM 19 C C5' GDD . . . P 2 21.449 -25.322 13.392 0.9 127.26 ? C5' GDD 401 E 1 HETATM 20 O O5' GDD . . . P 2 21.717 -24.761 14.694 0.9 131.03 ? O5' GDD 401 E 1 HETATM 21 P PA GDD . . . P 2 23.212 -24.719 15.289 0.9 149.07 ? PA GDD 401 E 1 HETATM 22 O O1A GDD . . . P 2 23.816 -23.372 15.183 0.9 136.7 ? O1A GDD 401 E 1 HETATM 23 O O2A GDD . . . P 2 23.972 -25.818 14.548 0.9 123.24 ? O2A GDD 401 E 1 HETATM 24 O O3A GDD . . . P 2 23.094 -25.184 16.808 0.9 150.53 ? O3A GDD 401 E 1 HETATM 25 P PB GDD . . . P 2 21.929 -25.816 17.694 0.9 158.76 ? PB GDD 401 E 1 HETATM 26 O O2B GDD . . . P 2 20.912 -26.437 16.733 0.9 134.61 ? O2B GDD 401 E 1 HETATM 27 O O3B GDD . . . P 2 22.475 -26.746 18.712 0.9 124.94 ? O3B GDD 401 E 1 HETATM 28 O O1B GDD . . . P 2 21.182 -24.535 18.384 0.9 144.83 ? O1B GDD 401 E 1 HETATM 29 C C11 GDD . . . P 2 19.814 -24.249 18.339 0.9 132.02 ? C11 GDD 401 E 1 HETATM 30 O O51 GDD . . . P 2 19.316 -23.979 19.636 0.9 131.4 ? O51 GDD 401 E 1 HETATM 31 C C51 GDD . . . P 2 19.973 -22.875 20.279 0.9 120.83 ? C51 GDD 401 E 1 HETATM 32 C C61 GDD . . . P 2 19.394 -22.783 21.672 0.9 111.99 ? C61 GDD 401 E 1 HETATM 33 O O6A GDD . . . P 2 19.799 -23.884 22.477 0.9 102.01 ? O6A GDD 401 E 1 HETATM 34 C C21 GDD . . . P 2 19.583 -23.052 17.426 0.9 126.83 ? C21 GDD 401 E 1 HETATM 35 O O21 GDD . . . P 2 18.188 -22.843 17.242 0.9 116.16 ? O21 GDD 401 E 1 HETATM 36 C C31 GDD . . . P 2 20.225 -21.808 18.026 0.9 129.31 ? C31 GDD 401 E 1 HETATM 37 O O31 GDD . . . P 2 19.895 -20.666 17.242 0.9 123.18 ? O31 GDD 401 E 1 HETATM 38 C C41 GDD . . . P 2 19.769 -21.6 19.465 0.9 120.81 ? C41 GDD 401 E 1 HETATM 39 O O41 GDD . . . P 2 20.521 -20.549 20.064 0.9 111.1 ? O41 GDD 401 E 1 HETATM 40 H H2N1 GDD . . . P 2 21.691 -33.369 10.594 0.9 112.55 ? H2N1 GDD 401 E 1 HETATM 41 H H2N2 GDD . . . P 2 22.245 -33.8 9.024 0.9 112.55 ? H2N2 GDD 401 E 1 HETATM 42 H H1 GDD . . . P 2 22.956 -32.164 7.543 0.9 115.72 ? H1 GDD 401 E 1 HETATM 43 H H8 GDD . . . P 2 22.225 -26.376 10.253 0.9 134.76 ? H8 GDD 401 E 1 HETATM 44 H H1' GDD . . . P 2 20.758 -29.301 12.23 0.9 139.37 ? H1' GDD 401 E 1 HETATM 45 H H2' GDD . . . P 2 23.318 -27.722 12.864 0.9 142.41 ? H2' GDD 401 E 1 HETATM 46 H HA GDD . . . P 2 23.33 -30.038 12.666 0.9 130.33 ? HA GDD 401 E 1 HETATM 47 H H3' GDD . . . P 2 22.349 -27.236 15.038 0.9 151.9 ? H3' GDD 401 E 1 HETATM 48 H HB GDD . . . P 2 21.501 -29.259 15.481 0.9 150.9 ? HB GDD 401 E 1 HETATM 49 H H4' GDD . . . P 2 19.851 -26.643 14.002 0.9 151.19 ? H4' GDD 401 E 1 HETATM 50 H "H5'1" GDD . . . P 2 22.367 -25.333 12.806 0.9 152.92 ? "H5'1" GDD 401 E 1 HETATM 51 H "H5'2" GDD . . . P 2 20.778 -24.597 12.934 0.9 152.92 ? "H5'2" GDD 401 E 1 HETATM 52 H HO2A GDD . . . P 2 24.474 -26.594 14.911 0.9 148.1 ? HO2A GDD 401 E 1 HETATM 53 H HO2B GDD . . . P 2 19.996 -26.184 16.445 0.9 161.73 ? HO2B GDD 401 E 1 HETATM 54 H H11 GDD . . . P 2 19.253 -25.139 18.058 0.9 158.64 ? H11 GDD 401 E 1 HETATM 55 H H51 GDD . . . P 2 21.035 -23.102 20.362 0.9 145.2 ? H51 GDD 401 E 1 HETATM 56 H H611 GDD . . . P 2 19.726 -21.843 22.112 0.9 134.6 ? H611 GDD 401 E 1 HETATM 57 H H612 GDD . . . P 2 18.307 -22.722 21.64 0.9 134.6 ? H612 GDD 401 E 1 HETATM 58 H H6A GDD . . . P 2 20.775 -23.762 22.611 0.9 122.62 ? H6A GDD 401 E 1 HETATM 59 H H21 GDD . . . P 2 20.001 -23.24 16.437 0.9 152.41 ? H21 GDD 401 E 1 HETATM 60 H HC GDD . . . P 2 18.051 -22.302 16.421 0.9 139.6 ? HC GDD 401 E 1 HETATM 61 H H31 GDD . . . P 2 21.311 -21.872 17.966 0.9 155.38 ? H31 GDD 401 E 1 HETATM 62 H HD GDD . . . P 2 20.134 -19.824 17.709 0.9 148.02 ? HD GDD 401 E 1 HETATM 63 H H41 GDD . . . P 2 18.71 -21.345 19.467 0.9 145.18 ? H41 GDD 401 E 1 HETATM 64 H HE GDD . . . P 2 21.478 -20.752 19.892 0.9 133.52 ? HE GDD 401 E 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 64 #