data_2GEJ # _model_server_result.job_id d0YXkLFHtOtdzSZ5nCnz2Q _model_server_result.datetime_utc '2024-12-26 10:22:36' _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 2gej # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":2567}' # _entry.id 2GEJ # _exptl.entry_id 2GEJ _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 1 _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 2GEJ _cell.length_a 37.071 _cell.length_b 72.747 _cell.length_c 137.166 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2GEJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 2GEJ _atom_sites.fract_transf_matrix[1][1] 0.02698 _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] 0.01375 _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] 0.00729 _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 B 2 GDD A 1 2567 2567 GDD GDD . C 3 HOH A 1 2568 2 HOH HOH . C 3 HOH A 2 2569 3 HOH HOH . C 3 HOH A 3 2570 4 HOH HOH . C 3 HOH A 4 2571 5 HOH HOH . C 3 HOH A 5 2572 6 HOH HOH . C 3 HOH A 6 2573 7 HOH HOH . C 3 HOH A 7 2574 8 HOH HOH . C 3 HOH A 8 2575 9 HOH HOH . C 3 HOH A 9 2576 10 HOH HOH . C 3 HOH A 10 2577 11 HOH HOH . C 3 HOH A 11 2578 12 HOH HOH . C 3 HOH A 12 2579 13 HOH HOH . C 3 HOH A 13 2580 14 HOH HOH . C 3 HOH A 14 2581 15 HOH HOH . C 3 HOH A 15 2582 16 HOH HOH . C 3 HOH A 16 2583 17 HOH HOH . C 3 HOH A 17 2584 18 HOH HOH . C 3 HOH A 18 2585 19 HOH HOH . C 3 HOH A 19 2586 20 HOH HOH . C 3 HOH A 20 2587 21 HOH HOH . C 3 HOH A 21 2588 22 HOH HOH . C 3 HOH A 22 2589 23 HOH HOH . C 3 HOH A 23 2590 24 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 . . . B 2 3.897 50.745 29.09 1 33.59 ? N2 GDD 2567 A 1 HETATM 2 C C2 GDD . . . B 2 2.785 50.218 29.562 1 33.26 ? C2 GDD 2567 A 1 HETATM 3 N N1 GDD . . . B 2 2.108 50.987 30.479 1 34.48 ? N1 GDD 2567 A 1 HETATM 4 N N3 GDD . . . B 2 2.34 49.006 29.188 1 31.97 ? N3 GDD 2567 A 1 HETATM 5 C C4 GDD . . . B 2 1.177 48.567 29.675 1 33.82 ? C4 GDD 2567 A 1 HETATM 6 C C5 GDD . . . B 2 0.421 49.313 30.589 1 34.48 ? C5 GDD 2567 A 1 HETATM 7 C C6 GDD . . . B 2 0.895 50.566 31.003 1 35.6 ? C6 GDD 2567 A 1 HETATM 8 O O6 GDD . . . B 2 0.298 51.309 31.809 1 35.65 ? O6 GDD 2567 A 1 HETATM 9 N N7 GDD . . . B 2 -0.679 48.596 30.904 1 34.56 ? N7 GDD 2567 A 1 HETATM 10 C C8 GDD . . . B 2 -0.629 47.446 30.211 1 35.18 ? C8 GDD 2567 A 1 HETATM 11 N N9 GDD . . . B 2 0.51 47.433 29.474 1 35.82 ? N9 GDD 2567 A 1 HETATM 12 C C1' GDD . . . B 2 0.903 46.389 28.56 1 34.05 ? C1' GDD 2567 A 1 HETATM 13 C C2' GDD . . . B 2 1.197 45.168 29.347 1 33.79 ? C2' GDD 2567 A 1 HETATM 14 O O2' GDD . . . B 2 2.558 45.282 29.714 1 40.84 ? O2' GDD 2567 A 1 HETATM 15 C C3' GDD . . . B 2 0.941 44.101 28.261 1 34.02 ? C3' GDD 2567 A 1 HETATM 16 O O3' GDD . . . B 2 2.016 43.944 27.305 1 32.61 ? O3' GDD 2567 A 1 HETATM 17 C C4' GDD . . . B 2 -0.268 44.701 27.479 1 33.08 ? C4' GDD 2567 A 1 HETATM 18 O O4' GDD . . . B 2 -0.373 46.072 27.933 1 33.41 ? O4' GDD 2567 A 1 HETATM 19 C C5' GDD . . . B 2 -1.54 43.927 27.804 1 30.26 ? C5' GDD 2567 A 1 HETATM 20 O O5' GDD . . . B 2 -1.691 43.704 29.171 1 29.98 ? O5' GDD 2567 A 1 HETATM 21 P PA GDD . . . B 2 -3.077 44.056 29.852 1 32.41 ? PA GDD 2567 A 1 HETATM 22 O O1A GDD . . . B 2 -3.142 43.455 31.251 1 30.01 ? O1A GDD 2567 A 1 HETATM 23 O O2A GDD . . . B 2 -3.366 45.533 29.842 1 33.92 ? O2A GDD 2567 A 1 HETATM 24 O O3A GDD . . . B 2 -4.067 43.049 29.053 1 34.69 ? O3A GDD 2567 A 1 HETATM 25 P PB GDD . . . B 2 -5.336 43.526 28.225 1 32.33 ? PB GDD 2567 A 1 HETATM 26 O O2B GDD . . . B 2 -6.319 44.12 29.423 1 33.58 ? O2B GDD 2567 A 1 HETATM 27 O O3B GDD . . . B 2 -4.992 44.501 27.184 1 32.4 ? O3B GDD 2567 A 1 HETATM 28 O O1B GDD . . . B 2 -5.963 42.174 27.688 1 33.15 ? O1B GDD 2567 A 1 HETATM 29 C C11 GDD . . . B 2 -5.377 41.496 26.596 1 31.67 ? C11 GDD 2567 A 1 HETATM 30 O O51 GDD . . . B 2 -4.013 41.141 27.033 1 31.32 ? O51 GDD 2567 A 1 HETATM 31 C C51 GDD . . . B 2 -3.944 40.068 28.026 1 32.62 ? C51 GDD 2567 A 1 HETATM 32 C C61 GDD . . . B 2 -2.451 39.931 28.076 1 29.99 ? C61 GDD 2567 A 1 HETATM 33 O O6A GDD . . . B 2 -2.102 38.774 27.393 1 29.58 ? O6A GDD 2567 A 1 HETATM 34 C C21 GDD . . . B 2 -6.311 40.311 26.286 1 30.95 ? C21 GDD 2567 A 1 HETATM 35 O O21 GDD . . . B 2 -5.85 39.613 25.162 1 34.2 ? O21 GDD 2567 A 1 HETATM 36 C C31 GDD . . . B 2 -6.271 39.266 27.378 1 33.48 ? C31 GDD 2567 A 1 HETATM 37 O O31 GDD . . . B 2 -7.134 38.145 27.026 1 32.72 ? O31 GDD 2567 A 1 HETATM 38 C C41 GDD . . . B 2 -4.777 38.828 27.626 1 33.72 ? C41 GDD 2567 A 1 HETATM 39 O O41 GDD . . . B 2 -4.7 37.828 28.665 1 32.16 ? O41 GDD 2567 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 39 #