data_4DA0 # _model_server_result.job_id AXnoYqVWMXBzB_EFGYkLbw _model_server_result.datetime_utc '2024-11-05 00:03:57' _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 4da0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 4DA0 # _exptl.entry_id 4DA0 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 267.241 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXY-GUANOSINE" _entity.pdbx_number_of_molecules 1 _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 4DA0 _cell.length_a 135.352 _cell.length_b 135.352 _cell.length_c 56.801 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DA0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_445 -y-1,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -67.676 -117.21827 0 3 'crystal symmetry operation' 3_545 -x+y,-x-1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 67.676 -117.21827 0 4 'crystal symmetry operation' 10_444 -y-1,-x-1,-z-1/2 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 -67.676 -117.21827 -28.4005 5 'crystal symmetry operation' 11_554 -x+y,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -28.4005 6 'crystal symmetry operation' 12_544 x,x-y-1,-z-1/2 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 67.676 -117.21827 -28.4005 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H13 N5 O4' _chem_comp.formula_weight 267.241 _chem_comp.id GNG _chem_comp.mon_nstd_flag n _chem_comp.name "2'-DEOXY-GUANOSINE" _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 O5' C5' GNG sing 129 n n O5' H5' GNG sing 130 n n C5' C4' GNG sing 131 n n C5' "H5'1" GNG sing 132 n n C5' "H5'2" GNG sing 133 n n C4' O4' GNG sing 134 n n C4' C3' GNG sing 135 n n C4' H4' GNG sing 136 n n O4' C1' GNG sing 137 n n C1' N9 GNG sing 138 n n C1' C2' GNG sing 139 n n C1' H1' GNG sing 140 n n N9 C8 GNG sing 141 n y N9 C4 GNG sing 142 n y C8 N7 GNG doub 143 n y C8 H8 GNG sing 144 n n N7 C5 GNG sing 145 n y C5 C4 GNG doub 146 n y C5 C6 GNG sing 147 n n C4 N3 GNG sing 148 n n N3 C2 GNG sing 149 n n N3 HN3 GNG sing 150 n n C2 N1 GNG doub 151 n n C2 N2 GNG sing 152 n n N1 C6 GNG sing 153 n n C6 O6 GNG doub 154 n n N2 HN21 GNG sing 155 n n N2 HN22 GNG sing 156 n n C2' C3' GNG sing 157 n n C2' "H2'1" GNG sing 158 n n C2' "H2'2" GNG sing 159 n n C3' O3' GNG sing 160 n n C3' H3' GNG sing 161 n n O3' H1 GNG sing 162 n n # _atom_sites.entry_id 4DA0 _atom_sites.fract_transf_matrix[1][1] 0.007388 _atom_sites.fract_transf_matrix[1][2] 0.004266 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008531 _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] 0.017605 _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 B 2 GNG A 1 301 1 GNG GNG . C 3 CL A 1 302 2 CL CL . # 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 O O5' GNG . . . B 2 -4.914 -51.739 -23.489 1 75.23 ? O5' GNG 301 A 1 HETATM 2 C C5' GNG . . . B 2 -4.925 -52.708 -22.429 1 75.75 ? C5' GNG 301 A 1 HETATM 3 C C4' GNG . . . B 2 -5.981 -52.377 -21.376 1 76.03 ? C4' GNG 301 A 1 HETATM 4 O O4' GNG . . . B 2 -7.231 -52.098 -21.994 1 77.22 ? O4' GNG 301 A 1 HETATM 5 C C1' GNG . . . B 2 -8.107 -53.226 -21.945 1 78.15 ? C1' GNG 301 A 1 HETATM 6 N N9 GNG . . . B 2 -8.251 -53.676 -23.366 1 80.86 ? N9 GNG 301 A 1 HETATM 7 C C8 GNG . . . B 2 -9.003 -52.973 -24.235 1 81.49 ? C8 GNG 301 A 1 HETATM 8 N N7 GNG . . . B 2 -9.001 -53.529 -25.465 1 82.07 ? N7 GNG 301 A 1 HETATM 9 C C5 GNG . . . B 2 -8.223 -54.621 -25.417 1 81.9 ? C5 GNG 301 A 1 HETATM 10 C C4 GNG . . . B 2 -7.714 -54.727 -24.036 1 81.78 ? C4 GNG 301 A 1 HETATM 11 N N3 GNG . . . B 2 -6.888 -55.78 -23.751 1 82.11 ? N3 GNG 301 A 1 HETATM 12 C C2 GNG . . . B 2 -6.541 -56.7 -24.695 1 81.83 ? C2 GNG 301 A 1 HETATM 13 N N1 GNG . . . B 2 -6.988 -56.643 -25.973 1 82.45 ? N1 GNG 301 A 1 HETATM 14 C C6 GNG . . . B 2 -7.813 -55.655 -26.399 1 82.5 ? C6 GNG 301 A 1 HETATM 15 O O6 GNG . . . B 2 -8.253 -55.606 -27.694 1 82.71 ? O6 GNG 301 A 1 HETATM 16 N N2 GNG . . . B 2 -5.723 -57.723 -24.366 1 81.73 ? N2 GNG 301 A 1 HETATM 17 C C2' GNG . . . B 2 -7.516 -54.225 -20.959 1 75.98 ? C2' GNG 301 A 1 HETATM 18 C C3' GNG . . . B 2 -6.272 -53.534 -20.442 1 75.84 ? C3' GNG 301 A 1 HETATM 19 O O3' GNG . . . B 2 -6.568 -52.956 -19.179 1 75.2 ? O3' GNG 301 A 1 # _model_server_stats.io_time_ms 42 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 19 #