data_5MN6 # _model_server_result.job_id aNt9lekgyngdjfG833vgbA _model_server_result.datetime_utc '2025-07-14 03:29:07' _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 5mn6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":401}' # _entry.id 5MN6 # _exptl.entry_id 5MN6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _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 5MN6 _cell.length_a 41.121 _cell.length_b 68.152 _cell.length_c 207.862 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5MN6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C 1 1 B,D 2 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 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 PB O1B GDP doub 70 n n PB O2B GDP sing 71 n n PB O3B GDP sing 72 n n PB O3A GDP sing 73 n n O2B HOB2 GDP sing 74 n n O3B HOB3 GDP sing 75 n n O3A PA GDP sing 76 n n PA O1A GDP doub 77 n n PA O2A GDP sing 78 n n PA O5' GDP sing 79 n n O2A HOA2 GDP sing 80 n n O5' C5' GDP sing 81 n n C5' C4' GDP sing 82 n n C5' H5' GDP sing 83 n n C5' "H5''" GDP sing 84 n n C4' O4' GDP sing 85 n n C4' C3' GDP sing 86 n n C4' H4' GDP sing 87 n n O4' C1' GDP sing 88 n n C3' O3' GDP sing 89 n n C3' C2' GDP sing 90 n n C3' H3' GDP sing 91 n n O3' HO3' GDP sing 92 n n C2' O2' GDP sing 93 n n C2' C1' GDP sing 94 n n C2' H2' GDP sing 95 n n O2' HO2' GDP sing 96 n n C1' N9 GDP sing 97 n n C1' H1' GDP sing 98 n n N9 C8 GDP sing 99 n y N9 C4 GDP sing 100 n y C8 N7 GDP doub 101 n y C8 H8 GDP sing 102 n n N7 C5 GDP sing 103 n y C5 C6 GDP sing 104 n n C5 C4 GDP doub 105 n y C6 O6 GDP doub 106 n n C6 N1 GDP sing 107 n n N1 C2 GDP sing 108 n n N1 HN1 GDP sing 109 n n C2 N2 GDP sing 110 n n C2 N3 GDP doub 111 n n N2 HN21 GDP sing 112 n n N2 HN22 GDP sing 113 n n N3 C4 GDP sing 114 n n # _atom_sites.entry_id 5MN6 _atom_sites.fract_transf_matrix[1][1] 0.024318 _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] 0.014673 _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] 0.004811 _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 GDP A 1 401 998 GDP GDP . D 2 GDP B 1 401 998 GDP GDP . # 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 P PB GDP . . . D 2 9.923 43.113 -23.386 1 114.5 ? PB GDP 401 B 1 HETATM 2 O O1B GDP . . . D 2 10.939 42.311 -24.168 1 95.75 ? O1B GDP 401 B 1 HETATM 3 O O2B GDP . . . D 2 8.95 42.343 -22.521 1 98.45 ? O2B GDP 401 B 1 HETATM 4 O O3B GDP . . . D 2 10.539 44.268 -22.621 1 114.29 ? O3B GDP 401 B 1 HETATM 5 O O3A GDP . . . D 2 9.045 43.802 -24.524 1 107.09 ? O3A GDP 401 B 1 HETATM 6 P PA GDP . . . D 2 7.478 43.532 -24.66 1 102.64 ? PA GDP 401 B 1 HETATM 7 O O1A GDP . . . D 2 7.363 42.066 -25.017 1 125.72 ? O1A GDP 401 B 1 HETATM 8 O O2A GDP . . . D 2 6.721 44.034 -23.444 1 105.13 ? O2A GDP 401 B 1 HETATM 9 O O5' GDP . . . D 2 7.131 44.453 -25.933 1 100.04 ? O5' GDP 401 B 1 HETATM 10 C C5' GDP . . . D 2 8.194 44.868 -26.792 1 102.81 ? C5' GDP 401 B 1 HETATM 11 C C4' GDP . . . D 2 7.754 45.08 -28.239 1 99.03 ? C4' GDP 401 B 1 HETATM 12 O O4' GDP . . . D 2 7.054 43.955 -28.777 1 98.76 ? O4' GDP 401 B 1 HETATM 13 C C3' GDP . . . D 2 6.835 46.268 -28.352 1 98.67 ? C3' GDP 401 B 1 HETATM 14 O O3' GDP . . . D 2 7.532 47.304 -29.02 1 120.59 ? O3' GDP 401 B 1 HETATM 15 C C2' GDP . . . D 2 5.657 45.814 -29.172 1 90.53 ? C2' GDP 401 B 1 HETATM 16 O O2' GDP . . . D 2 5.702 46.345 -30.481 1 91.36 ? O2' GDP 401 B 1 HETATM 17 C C1' GDP . . . D 2 5.794 44.332 -29.327 1 89.12 ? C1' GDP 401 B 1 HETATM 18 N N9 GDP . . . D 2 4.71 43.703 -28.54 1 91.74 ? N9 GDP 401 B 1 HETATM 19 C C8 GDP . . . D 2 4.139 44.167 -27.4 1 84.24 ? C8 GDP 401 B 1 HETATM 20 N N7 GDP . . . D 2 3.196 43.302 -26.966 1 94.3 ? N7 GDP 401 B 1 HETATM 21 C C5 GDP . . . D 2 3.153 42.271 -27.837 1 95.04 ? C5 GDP 401 B 1 HETATM 22 C C6 GDP . . . D 2 2.383 41.017 -27.989 1 90.64 ? C6 GDP 401 B 1 HETATM 23 O O6 GDP . . . D 2 1.517 40.684 -27.174 1 95.55 ? O6 GDP 401 B 1 HETATM 24 N N1 GDP . . . D 2 2.644 40.238 -29.042 1 91.33 ? N1 GDP 401 B 1 HETATM 25 C C2 GDP . . . D 2 3.578 40.529 -29.964 1 96 ? C2 GDP 401 B 1 HETATM 26 N N2 GDP . . . D 2 3.779 39.674 -30.988 1 102.25 ? N2 GDP 401 B 1 HETATM 27 N N3 GDP . . . D 2 4.322 41.656 -29.902 1 101.12 ? N3 GDP 401 B 1 HETATM 28 C C4 GDP . . . D 2 4.157 42.539 -28.877 1 95.69 ? C4 GDP 401 B 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 338 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #