data_3HKC # _model_server_result.job_id -rg0nOo62JjrC4CElscWGg _model_server_result.datetime_utc '2024-11-14 07:09:28' _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 3hkc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":600}' # _entry.id 3HKC # _exptl.entry_id 3HKC _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 3HKC _cell.length_a 329.24 _cell.length_b 329.24 _cell.length_c 53.87 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3HKC _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 128 n n PB O2B GDP sing 129 n n PB O3B GDP sing 130 n n PB O3A GDP sing 131 n n O2B HOB2 GDP sing 132 n n O3B HOB3 GDP sing 133 n n O3A PA GDP sing 134 n n PA O1A GDP doub 135 n n PA O2A GDP sing 136 n n PA O5' GDP sing 137 n n O2A HOA2 GDP sing 138 n n O5' C5' GDP sing 139 n n C5' C4' GDP sing 140 n n C5' H5' GDP sing 141 n n C5' "H5''" GDP sing 142 n n C4' O4' GDP sing 143 n n C4' C3' GDP sing 144 n n C4' H4' GDP sing 145 n n O4' C1' GDP sing 146 n n C3' O3' GDP sing 147 n n C3' C2' GDP sing 148 n n C3' H3' GDP sing 149 n n O3' HO3' GDP sing 150 n n C2' O2' GDP sing 151 n n C2' C1' GDP sing 152 n n C2' H2' GDP sing 153 n n O2' HO2' GDP sing 154 n n C1' N9 GDP sing 155 n n C1' H1' GDP sing 156 n n N9 C8 GDP sing 157 n y N9 C4 GDP sing 158 n y C8 N7 GDP doub 159 n y C8 H8 GDP sing 160 n n N7 C5 GDP sing 161 n y C5 C6 GDP sing 162 n n C5 C4 GDP doub 163 n y C6 O6 GDP doub 164 n n C6 N1 GDP sing 165 n n N1 C2 GDP sing 166 n n N1 HN1 GDP sing 167 n n C2 N2 GDP sing 168 n n C2 N3 GDP doub 169 n n N2 HN21 GDP sing 170 n n N2 HN22 GDP sing 171 n n N3 C4 GDP sing 172 n n # _atom_sites.entry_id 3HKC _atom_sites.fract_transf_matrix[1][1] 0.003037 _atom_sites.fract_transf_matrix[1][2] 0.001754 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003507 _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] 0.018563 _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 E70 B 1 700 700 E70 E70 . 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 E70 D 1 700 700 E70 E70 . # 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 . . . H 6 90.39 72.455 5.492 1 52.68 ? PB GDP 600 B 1 HETATM 2 O O1B GDP . . . H 6 91.329 73.159 6.408 1 51.81 ? O1B GDP 600 B 1 HETATM 3 O O2B GDP . . . H 6 90.78 70.966 5.4 1 52.09 ? O2B GDP 600 B 1 HETATM 4 O O3B GDP . . . H 6 88.893 72.568 5.929 1 51.71 ? O3B GDP 600 B 1 HETATM 5 O O3A GDP . . . H 6 90.584 73.163 4.068 1 51.56 ? O3A GDP 600 B 1 HETATM 6 P PA GDP . . . H 6 91.259 72.355 2.872 1 50.55 ? PA GDP 600 B 1 HETATM 7 O O1A GDP . . . H 6 92.451 71.708 3.447 1 49.92 ? O1A GDP 600 B 1 HETATM 8 O O2A GDP . . . H 6 90.276 71.382 2.176 1 50.61 ? O2A GDP 600 B 1 HETATM 9 O O5' GDP . . . H 6 91.667 73.574 1.906 1 51.09 ? O5' GDP 600 B 1 HETATM 10 C C5' GDP . . . H 6 90.823 73.953 0.835 1 51.9 ? C5' GDP 600 B 1 HETATM 11 C C4' GDP . . . H 6 91.57 74.88 -0.123 1 51.67 ? C4' GDP 600 B 1 HETATM 12 O O4' GDP . . . H 6 92.964 74.745 0.021 1 50.91 ? O4' GDP 600 B 1 HETATM 13 C C3' GDP . . . H 6 91.234 74.568 -1.568 1 51.96 ? C3' GDP 600 B 1 HETATM 14 O O3' GDP . . . H 6 90.733 75.738 -2.157 1 52.76 ? O3' GDP 600 B 1 HETATM 15 C C2' GDP . . . H 6 92.533 74.2 -2.255 1 51.45 ? C2' GDP 600 B 1 HETATM 16 O O2' GDP . . . H 6 92.819 74.985 -3.403 1 51.4 ? O2' GDP 600 B 1 HETATM 17 C C1' GDP . . . H 6 93.594 74.356 -1.187 1 51.21 ? C1' GDP 600 B 1 HETATM 18 N N9 GDP . . . H 6 94.284 73.061 -1.02 1 51.06 ? N9 GDP 600 B 1 HETATM 19 C C8 GDP . . . H 6 93.684 71.879 -0.679 1 51.42 ? C8 GDP 600 B 1 HETATM 20 N N7 GDP . . . H 6 94.625 70.908 -0.617 1 51.37 ? N7 GDP 600 B 1 HETATM 21 C C5 GDP . . . H 6 95.827 71.452 -0.906 1 51.15 ? C5 GDP 600 B 1 HETATM 22 C C6 GDP . . . H 6 97.102 70.897 -0.995 1 50.97 ? C6 GDP 600 B 1 HETATM 23 O O6 GDP . . . H 6 97.162 69.684 -1.203 1 50.92 ? O6 GDP 600 B 1 HETATM 24 N N1 GDP . . . H 6 98.187 71.711 -1.324 1 49.95 ? N1 GDP 600 B 1 HETATM 25 C C2 GDP . . . H 6 98.001 73.06 -1.577 1 49.41 ? C2 GDP 600 B 1 HETATM 26 N N2 GDP . . . H 6 98.86 73.682 -2.367 1 48.52 ? N2 GDP 600 B 1 HETATM 27 N N3 GDP . . . H 6 96.727 73.591 -1.492 1 50.51 ? N3 GDP 600 B 1 HETATM 28 C C4 GDP . . . H 6 95.641 72.807 -1.174 1 51.18 ? C4 GDP 600 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 370 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 28 #