data_3HKD # _model_server_result.job_id jg8gSdCuMaLF55FtdjjCNQ _model_server_result.datetime_utc '2025-02-17 23:29:50' _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 3hkd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":600}' # _entry.id 3HKD # _exptl.entry_id 3HKD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 6 _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 120 _cell.entry_id 3HKD _cell.length_a 328.53 _cell.length_b 328.53 _cell.length_c 54.41 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3HKD _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 H N N ? 6 M 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 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 3HKD _atom_sites.fract_transf_matrix[1][1] 0.003044 _atom_sites.fract_transf_matrix[1][2] 0.001757 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003515 _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] 0.018379 _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 F 4 GTP A 1 600 600 GTP GTP . G 5 MG A 1 601 601 MG MG . H 6 GDP B 1 600 600 GDP GDP . I 5 MG B 1 601 601 MG MG . J 7 N16 B 1 700 700 N16 N16 . K 4 GTP C 1 600 600 GTP GTP . L 5 MG C 1 601 601 MG MG . M 6 GDP D 1 600 600 GDP GDP . N 7 N16 D 1 700 700 N16 N16 . # 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 . . . M 6 11.495 42.609 -2.131 1 41.55 ? PB GDP 600 D 1 HETATM 2 O O1B GDP . . . M 6 12.779 42.953 -1.459 1 40.1 ? O1B GDP 600 D 1 HETATM 3 O O2B GDP . . . M 6 11.318 41.095 -2.268 1 41.18 ? O2B GDP 600 D 1 HETATM 4 O O3B GDP . . . M 6 10.219 43.094 -1.411 1 41.28 ? O3B GDP 600 D 1 HETATM 5 O O3A GDP . . . M 6 11.588 43.337 -3.561 1 43.19 ? O3A GDP 600 D 1 HETATM 6 P PA GDP . . . M 6 11.344 42.572 -4.949 1 44.55 ? PA GDP 600 D 1 HETATM 7 O O1A GDP . . . M 6 11.68 41.149 -4.774 1 44.24 ? O1A GDP 600 D 1 HETATM 8 O O2A GDP . . . M 6 9.88 42.714 -5.438 1 44.75 ? O2A GDP 600 D 1 HETATM 9 O O5' GDP . . . M 6 12.395 43.253 -5.97 1 45.28 ? O5' GDP 600 D 1 HETATM 10 C C5' GDP . . . M 6 12.317 44.639 -6.238 1 47.14 ? C5' GDP 600 D 1 HETATM 11 C C4' GDP . . . M 6 12.116 44.971 -7.711 1 48.89 ? C4' GDP 600 D 1 HETATM 12 O O4' GDP . . . M 6 13.266 44.677 -8.486 1 50.3 ? O4' GDP 600 D 1 HETATM 13 C C3' GDP . . . M 6 10.959 44.207 -8.337 1 48.89 ? C3' GDP 600 D 1 HETATM 14 O O3' GDP . . . M 6 9.754 44.894 -8.139 1 49 ? O3' GDP 600 D 1 HETATM 15 C C2' GDP . . . M 6 11.352 44.135 -9.8 1 49.45 ? C2' GDP 600 D 1 HETATM 16 O O2' GDP . . . M 6 10.927 45.293 -10.533 1 49.76 ? O2' GDP 600 D 1 HETATM 17 C C1' GDP . . . M 6 12.873 44.079 -9.714 1 50.88 ? C1' GDP 600 D 1 HETATM 18 N N9 GDP . . . M 6 13.275 42.672 -9.607 1 53.17 ? N9 GDP 600 D 1 HETATM 19 C C8 GDP . . . M 6 12.497 41.694 -9.04 1 54.36 ? C8 GDP 600 D 1 HETATM 20 N N7 GDP . . . M 6 13.2 40.547 -9.092 1 56.25 ? N7 GDP 600 D 1 HETATM 21 C C5 GDP . . . M 6 14.415 40.766 -9.66 1 55.91 ? C5 GDP 600 D 1 HETATM 22 C C6 GDP . . . M 6 15.475 39.903 -9.957 1 56.5 ? C6 GDP 600 D 1 HETATM 23 O O6 GDP . . . M 6 15.121 38.761 -10.36 1 56.97 ? O6 GDP 600 D 1 HETATM 24 N N1 GDP . . . M 6 16.612 40.448 -10.548 1 56.62 ? N1 GDP 600 D 1 HETATM 25 C C2 GDP . . . M 6 16.68 41.778 -10.912 1 56.64 ? C2 GDP 600 D 1 HETATM 26 N N2 GDP . . . M 6 17.263 42 -12.094 1 57.66 ? N2 GDP 600 D 1 HETATM 27 N N3 GDP . . . M 6 15.599 42.597 -10.603 1 56.09 ? N3 GDP 600 D 1 HETATM 28 C C4 GDP . . . M 6 14.475 42.108 -10.002 1 54.93 ? C4 GDP 600 D 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 352 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 28 #