data_3HKD # _model_server_result.job_id iS1eV4RMYtiyYicHd7jbqg _model_server_result.datetime_utc '2024-11-14 06:25:21' _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":"K","auth_seq_id":600}' # _entry.id 3HKD # _exptl.entry_id 3HKD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.18 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-TRIPHOSPHATE" _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 ? 4 F N N ? 4 K N N # _chem_comp.formula 'C10 H16 N5 O14 P3' _chem_comp.formula_weight 523.18 _chem_comp.id GTP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-TRIPHOSPHATE" _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 PG O1G GTP doub 174 n n PG O2G GTP sing 175 n n PG O3G GTP sing 176 n n PG O3B GTP sing 177 n n O2G HOG2 GTP sing 178 n n O3G HOG3 GTP sing 179 n n O3B PB GTP sing 180 n n PB O1B GTP doub 181 n n PB O2B GTP sing 182 n n PB O3A GTP sing 183 n n O2B HOB2 GTP sing 184 n n O3A PA GTP sing 185 n n PA O1A GTP doub 186 n n PA O2A GTP sing 187 n n PA O5' GTP sing 188 n n O2A HOA2 GTP sing 189 n n O5' C5' GTP sing 190 n n C5' C4' GTP sing 191 n n C5' H5' GTP sing 192 n n C5' "H5''" GTP sing 193 n n C4' O4' GTP sing 194 n n C4' C3' GTP sing 195 n n C4' H4' GTP sing 196 n n O4' C1' GTP sing 197 n n C3' O3' GTP sing 198 n n C3' C2' GTP sing 199 n n C3' H3' GTP sing 200 n n O3' HO3' GTP sing 201 n n C2' O2' GTP sing 202 n n C2' C1' GTP sing 203 n n C2' H2' GTP sing 204 n n O2' HO2' GTP sing 205 n n C1' N9 GTP sing 206 n n C1' H1' GTP sing 207 n n N9 C8 GTP sing 208 n y N9 C4 GTP sing 209 n y C8 N7 GTP doub 210 n y C8 H8 GTP sing 211 n n N7 C5 GTP sing 212 n y C5 C6 GTP sing 213 n n C5 C4 GTP doub 214 n y C6 O6 GTP doub 215 n n C6 N1 GTP sing 216 n n N1 C2 GTP sing 217 n n N1 HN1 GTP sing 218 n n C2 N2 GTP sing 219 n n C2 N3 GTP doub 220 n n N2 HN21 GTP sing 221 n n N2 HN22 GTP sing 222 n n N3 C4 GTP sing 223 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 PG GTP . . . K 4 50.263 53.227 0.062 1 29.87 ? PG GTP 600 C 1 HETATM 2 O O1G GTP . . . K 4 50.358 52.22 -1.026 1 29.62 ? O1G GTP 600 C 1 HETATM 3 O O2G GTP . . . K 4 50.196 52.471 1.394 1 30.13 ? O2G GTP 600 C 1 HETATM 4 O O3G GTP . . . K 4 49.004 54.118 -0.003 1 29.67 ? O3G GTP 600 C 1 HETATM 5 O O3B GTP . . . K 4 51.55 54.181 -0.026 1 27.33 ? O3B GTP 600 C 1 HETATM 6 P PB GTP . . . K 4 51.254 55.733 -0.263 1 25.25 ? PB GTP 600 C 1 HETATM 7 O O1B GTP . . . K 4 52.382 56.512 0.253 1 24.6 ? O1B GTP 600 C 1 HETATM 8 O O2B GTP . . . K 4 49.933 56.13 0.42 1 24.97 ? O2B GTP 600 C 1 HETATM 9 O O3A GTP . . . K 4 51.107 55.855 -1.865 1 27.84 ? O3A GTP 600 C 1 HETATM 10 P PA GTP . . . K 4 52.299 55.712 -2.954 1 29.47 ? PA GTP 600 C 1 HETATM 11 O O1A GTP . . . K 4 51.92 54.86 -4.112 1 29.7 ? O1A GTP 600 C 1 HETATM 12 O O2A GTP . . . K 4 53.551 55.122 -2.273 1 30.39 ? O2A GTP 600 C 1 HETATM 13 O O5' GTP . . . K 4 52.478 57.224 -3.487 1 29.65 ? O5' GTP 600 C 1 HETATM 14 C C5' GTP . . . K 4 51.82 57.66 -4.658 1 31.57 ? C5' GTP 600 C 1 HETATM 15 C C4' GTP . . . K 4 52.795 57.773 -5.822 1 32.74 ? C4' GTP 600 C 1 HETATM 16 O O4' GTP . . . K 4 53.654 56.666 -5.805 1 32.8 ? O4' GTP 600 C 1 HETATM 17 C C3' GTP . . . K 4 52.129 57.731 -7.19 1 33.16 ? C3' GTP 600 C 1 HETATM 18 O O3' GTP . . . K 4 52.629 58.843 -7.899 1 33.5 ? O3' GTP 600 C 1 HETATM 19 C C2' GTP . . . K 4 52.596 56.445 -7.835 1 32.91 ? C2' GTP 600 C 1 HETATM 20 O O2' GTP . . . K 4 52.8 56.619 -9.213 1 32.21 ? O2' GTP 600 C 1 HETATM 21 C C1' GTP . . . K 4 53.925 56.33 -7.136 1 33.55 ? C1' GTP 600 C 1 HETATM 22 N N9 GTP . . . K 4 54.611 55.046 -7.121 1 35.23 ? N9 GTP 600 C 1 HETATM 23 C C8 GTP . . . K 4 54.188 53.88 -6.541 1 36.31 ? C8 GTP 600 C 1 HETATM 24 N N7 GTP . . . K 4 55.165 52.954 -6.734 1 37.42 ? N7 GTP 600 C 1 HETATM 25 C C5 GTP . . . K 4 56.209 53.521 -7.403 1 36.72 ? C5 GTP 600 C 1 HETATM 26 C C6 GTP . . . K 4 57.446 53.05 -7.857 1 36.05 ? C6 GTP 600 C 1 HETATM 27 O O6 GTP . . . K 4 57.78 51.892 -7.665 1 36.21 ? O6 GTP 600 C 1 HETATM 28 N N1 GTP . . . K 4 58.314 53.882 -8.535 1 35.63 ? N1 GTP 600 C 1 HETATM 29 C C2 GTP . . . K 4 57.968 55.2 -8.767 1 35.83 ? C2 GTP 600 C 1 HETATM 30 N N2 GTP . . . K 4 58.804 56.012 -9.416 1 34.83 ? N2 GTP 600 C 1 HETATM 31 N N3 GTP . . . K 4 56.744 55.665 -8.31 1 36.45 ? N3 GTP 600 C 1 HETATM 32 C C4 GTP . . . K 4 55.871 54.847 -7.645 1 36.33 ? C4 GTP 600 C 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 242 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 32 #