data_3HKB # _model_server_result.job_id 2pElHgJhKOI8KmUoN0c3WQ _model_server_result.datetime_utc '2024-11-13 06:53:15' _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 3hkb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":600}' # _entry.id 3HKB # _exptl.entry_id 3HKB _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 3HKB _cell.length_a 328.826 _cell.length_b 328.826 _cell.length_c 53.711 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3HKB _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 _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 K 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 3HKB _atom_sites.fract_transf_matrix[1][1] 0.003041 _atom_sites.fract_transf_matrix[1][2] 0.001756 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003512 _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] 0.018618 _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 4 GTP C 1 600 600 GTP GTP . J 5 MG C 1 601 601 MG MG . K 6 GDP D 1 600 600 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 . . . K 6 11.841 42.001 -3.371 1 62.98 ? PB GDP 600 D 1 HETATM 2 O O1B GDP . . . K 6 12.757 42.825 -2.554 1 62.25 ? O1B GDP 600 D 1 HETATM 3 O O2B GDP . . . K 6 12.483 40.609 -3.475 1 62.91 ? O2B GDP 600 D 1 HETATM 4 O O3B GDP . . . K 6 10.407 41.844 -2.774 1 61.48 ? O3B GDP 600 D 1 HETATM 5 O O3A GDP . . . K 6 11.802 42.741 -4.812 1 63.23 ? O3A GDP 600 D 1 HETATM 6 P PA GDP . . . K 6 12.143 41.975 -6.202 1 63.31 ? PA GDP 600 D 1 HETATM 7 O O1A GDP . . . K 6 13.418 41.274 -5.977 1 63.59 ? O1A GDP 600 D 1 HETATM 8 O O2A GDP . . . K 6 11.03 40.984 -6.619 1 63.61 ? O2A GDP 600 D 1 HETATM 9 O O5' GDP . . . K 6 12.363 43.093 -7.345 1 61.99 ? O5' GDP 600 D 1 HETATM 10 C C5' GDP . . . K 6 11.342 43.916 -7.875 1 60.34 ? C5' GDP 600 D 1 HETATM 11 C C4' GDP . . . K 6 11.979 44.716 -9.005 1 59.47 ? C4' GDP 600 D 1 HETATM 12 O O4' GDP . . . K 6 13.224 44.137 -9.314 1 58.6 ? O4' GDP 600 D 1 HETATM 13 C C3' GDP . . . K 6 11.179 44.695 -10.3 1 59.97 ? C3' GDP 600 D 1 HETATM 14 O O3' GDP . . . K 6 11.135 46 -10.818 1 61.83 ? O3' GDP 600 D 1 HETATM 15 C C2' GDP . . . K 6 11.937 43.853 -11.3 1 58.85 ? C2' GDP 600 D 1 HETATM 16 O O2' GDP . . . K 6 12.105 44.506 -12.544 1 58.87 ? O2' GDP 600 D 1 HETATM 17 C C1' GDP . . . K 6 13.278 43.65 -10.646 1 57.97 ? C1' GDP 600 D 1 HETATM 18 N N9 GDP . . . K 6 13.626 42.231 -10.624 1 56.65 ? N9 GDP 600 D 1 HETATM 19 C C8 GDP . . . K 6 12.943 41.235 -10.004 1 56.22 ? C8 GDP 600 D 1 HETATM 20 N N7 GDP . . . K 6 13.62 40.091 -10.216 1 56.67 ? N7 GDP 600 D 1 HETATM 21 C C5 GDP . . . K 6 14.716 40.345 -10.949 1 56.74 ? C5 GDP 600 D 1 HETATM 22 C C6 GDP . . . K 6 15.734 39.541 -11.431 1 57.45 ? C6 GDP 600 D 1 HETATM 23 O O6 GDP . . . K 6 15.746 38.336 -11.17 1 58.39 ? O6 GDP 600 D 1 HETATM 24 N N1 GDP . . . K 6 16.753 40.116 -12.169 1 57.43 ? N1 GDP 600 D 1 HETATM 25 C C2 GDP . . . K 6 16.756 41.474 -12.424 1 56.41 ? C2 GDP 600 D 1 HETATM 26 N N2 GDP . . . K 6 17.79 42.058 -13.02 1 55.44 ? N2 GDP 600 D 1 HETATM 27 N N3 GDP . . . K 6 15.736 42.251 -11.935 1 56.43 ? N3 GDP 600 D 1 HETATM 28 C C4 GDP . . . K 6 14.732 41.696 -11.214 1 56.55 ? C4 GDP 600 D 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 251 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #