data_5OGK # _model_server_result.job_id 5-Mto04mlKo3KRXMONJQug _model_server_result.datetime_utc '2025-03-06 21:33:02' _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":"N","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 . . . N 2 4.938 -13.778 -27.177 0.77 77.13 ? N2 GDD 401 D 1 HETATM 2 C C2 GDD . . . N 2 5.408 -15.019 -27.036 0.77 84.51 ? C2 GDD 401 D 1 HETATM 3 N N1 GDD . . . N 2 6.222 -15.256 -25.96 0.77 85.13 ? N1 GDD 401 D 1 HETATM 4 N N3 GDD . . . N 2 5.078 -15.953 -27.924 0.77 85.45 ? N3 GDD 401 D 1 HETATM 5 C C4 GDD . . . N 2 5.632 -17.151 -27.65 0.77 84.89 ? C4 GDD 401 D 1 HETATM 6 C C5 GDD . . . N 2 6.459 -17.486 -26.599 0.77 81.3 ? C5 GDD 401 D 1 HETATM 7 C C6 GDD . . . N 2 6.803 -16.471 -25.653 0.77 81.65 ? C6 GDD 401 D 1 HETATM 8 O O6 GDD . . . N 2 7.518 -16.59 -24.66 0.77 82.69 ? O6 GDD 401 D 1 HETATM 9 N N7 GDD . . . N 2 6.813 -18.824 -26.668 0.77 79.93 ? N7 GDD 401 D 1 HETATM 10 C C8 GDD . . . N 2 6.202 -19.266 -27.743 0.77 85.6 ? C8 GDD 401 D 1 HETATM 11 N N9 GDD . . . N 2 5.469 -18.301 -28.384 0.77 86.4 ? N9 GDD 401 D 1 HETATM 12 C C1' GDD . . . N 2 4.665 -18.458 -29.608 0.77 88.53 ? C1' GDD 401 D 1 HETATM 13 C C2' GDD . . . N 2 5.507 -18.546 -30.883 0.77 90.84 ? C2' GDD 401 D 1 HETATM 14 O O2' GDD . . . N 2 5.684 -17.259 -31.463 0.77 84.49 ? O2' GDD 401 D 1 HETATM 15 C C3' GDD . . . N 2 4.632 -19.447 -31.756 0.77 96.68 ? C3' GDD 401 D 1 HETATM 16 O O3' GDD . . . N 2 3.59 -18.725 -32.402 0.77 93.72 ? O3' GDD 401 D 1 HETATM 17 C C4' GDD . . . N 2 4.061 -20.427 -30.736 0.77 95.12 ? C4' GDD 401 D 1 HETATM 18 O O4' GDD . . . N 2 3.943 -19.674 -29.509 0.77 91.92 ? O4' GDD 401 D 1 HETATM 19 C C5' GDD . . . N 2 4.888 -21.663 -30.489 0.77 92.95 ? C5' GDD 401 D 1 HETATM 20 O O5' GDD . . . N 2 4.596 -22.634 -31.517 0.77 101.05 ? O5' GDD 401 D 1 HETATM 21 P PA GDD . . . N 2 5.266 -22.622 -32.989 0.77 114.13 ? PA GDD 401 D 1 HETATM 22 O O1A GDD . . . N 2 5.417 -23.996 -33.519 0.77 106.49 ? O1A GDD 401 D 1 HETATM 23 O O2A GDD . . . N 2 6.578 -21.837 -32.89 0.77 104.17 ? O2A GDD 401 D 1 HETATM 24 O O3A GDD . . . N 2 4.268 -21.756 -33.879 0.77 116.97 ? O3A GDD 401 D 1 HETATM 25 P PB GDD . . . N 2 4.378 -21.014 -35.285 0.77 123.5 ? PB GDD 401 D 1 HETATM 26 O O2B GDD . . . N 2 3.213 -20.024 -35.355 0.77 107.95 ? O2B GDD 401 D 1 HETATM 27 O O3B GDD . . . N 2 5.698 -20.368 -35.447 0.77 107.54 ? O3B GDD 401 D 1 HETATM 28 O O1B GDD . . . N 2 4.109 -22.165 -36.43 0.77 111.57 ? O1B GDD 401 D 1 HETATM 29 C C11 GDD . . . N 2 2.879 -22.779 -36.733 0.77 100.75 ? C11 GDD 401 D 1 HETATM 30 O O51 GDD . . . N 2 2.652 -22.845 -38.132 0.77 94.7 ? O51 GDD 401 D 1 HETATM 31 C C51 GDD . . . N 2 3.601 -23.665 -38.834 0.77 93.46 ? C51 GDD 401 D 1 HETATM 32 C C61 GDD . . . N 2 3.287 -23.537 -40.307 0.77 84.19 ? C61 GDD 401 D 1 HETATM 33 O O6A GDD . . . N 2 4.176 -24.315 -41.097 0.77 78.51 ? O6A GDD 401 D 1 HETATM 34 C C21 GDD . . . N 2 2.817 -24.169 -36.106 0.77 100.58 ? C21 GDD 401 D 1 HETATM 35 O O21 GDD . . . N 2 1.483 -24.664 -36.147 0.77 83.56 ? O21 GDD 401 D 1 HETATM 36 C C31 GDD . . . N 2 3.754 -25.131 -36.827 0.77 100.94 ? C31 GDD 401 D 1 HETATM 37 O O31 GDD . . . N 2 3.571 -26.453 -36.331 0.77 92.46 ? O31 GDD 401 D 1 HETATM 38 C C41 GDD . . . N 2 3.505 -25.101 -38.327 0.77 97.49 ? C41 GDD 401 D 1 HETATM 39 O O41 GDD . . . N 2 4.468 -25.903 -39 0.77 98.04 ? O41 GDD 401 D 1 HETATM 40 H H2N1 GDD . . . N 2 4.33 -13.544 -27.955 0.77 92.76 ? H2N1 GDD 401 D 1 HETATM 41 H H2N2 GDD . . . N 2 5.151 -13.018 -26.539 0.77 92.76 ? H2N2 GDD 401 D 1 HETATM 42 H H1 GDD . . . N 2 6.44 -14.504 -25.314 0.77 102.37 ? H1 GDD 401 D 1 HETATM 43 H H8 GDD . . . N 2 6.268 -20.295 -28.093 0.77 102.93 ? H8 GDD 401 D 1 HETATM 44 H H1' GDD . . . N 2 3.941 -17.646 -29.642 0.77 106.45 ? H1' GDD 401 D 1 HETATM 45 H H2' GDD . . . N 2 6.473 -19.009 -30.691 0.77 109.22 ? H2' GDD 401 D 1 HETATM 46 H HA GDD . . . N 2 6.645 -17.039 -31.343 0.77 101.6 ? HA GDD 401 D 1 HETATM 47 H H3' GDD . . . N 2 5.22 -19.961 -32.515 0.77 116.22 ? H3' GDD 401 D 1 HETATM 48 H HB GDD . . . N 2 4.033 -18.143 -33.075 0.77 112.67 ? HB GDD 401 D 1 HETATM 49 H H4' GDD . . . N 2 3.033 -20.678 -30.996 0.77 114.36 ? H4' GDD 401 D 1 HETATM 50 H "H5'1" GDD . . . N 2 5.958 -21.461 -30.474 0.77 111.75 ? "H5'1" GDD 401 D 1 HETATM 51 H "H5'2" GDD . . . N 2 4.641 -22.184 -29.565 0.77 111.75 ? "H5'2" GDD 401 D 1 HETATM 52 H HO2A GDD . . . N 2 7.255 -21.648 -33.591 0.77 125.21 ? HO2A GDD 401 D 1 HETATM 53 H HO2B GDD . . . N 2 3.095 -19.081 -35.065 0.77 129.75 ? HO2B GDD 401 D 1 HETATM 54 H H11 GDD . . . N 2 2.065 -22.128 -36.416 0.77 121.11 ? H11 GDD 401 D 1 HETATM 55 H H51 GDD . . . N 2 4.601 -23.271 -38.658 0.77 112.36 ? H51 GDD 401 D 1 HETATM 56 H H611 GDD . . . N 2 2.257 -23.858 -40.459 0.77 101.24 ? H611 GDD 401 D 1 HETATM 57 H H612 GDD . . . N 2 3.318 -22.495 -40.623 0.77 101.24 ? H612 GDD 401 D 1 HETATM 58 H H6A GDD . . . N 2 3.818 -24.261 -42.022 0.77 94.42 ? H6A GDD 401 D 1 HETATM 59 H H21 GDD . . . N 2 3.09 -24.119 -35.053 0.77 120.91 ? H21 GDD 401 D 1 HETATM 60 H HC GDD . . . N 2 1.226 -24.969 -35.238 0.77 100.48 ? HC GDD 401 D 1 HETATM 61 H H31 GDD . . . N 2 4.792 -24.897 -36.598 0.77 121.34 ? H31 GDD 401 D 1 HETATM 62 H HD GDD . . . N 2 2.608 -26.662 -36.202 0.77 111.16 ? HD GDD 401 D 1 HETATM 63 H H41 GDD . . . N 2 2.503 -25.479 -38.527 0.77 117.19 ? H41 GDD 401 D 1 HETATM 64 H HE GDD . . . N 2 4.102 -26.826 -39.025 0.77 117.85 ? HE GDD 401 D 1 # _model_server_stats.io_time_ms 43 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 350 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 64 #