data_4BZC # _model_server_result.job_id 9QS7yYcWkGNyU4y-nM4S6A _model_server_result.datetime_utc '2024-11-07 02:42:15' _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 4bzc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":800}' # _entry.id 4BZC # _exptl.entry_id 4BZC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.247 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-deoxyguanosine-5'-O-(1-thiotriphosphate)" _entity.pdbx_number_of_molecules 12 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 113.56 _cell.angle_gamma 90 _cell.entry_id 4BZC _cell.length_a 79.002 _cell.length_b 138.727 _cell.length_c 93.715 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4BZC _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,O,P,Q,R,S,T,U,V,W,X,Y,Z,AA,BA _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 ? 2 E N N ? 2 G N N ? 2 H N N ? 2 J N N ? 2 L N N ? 2 M N N ? 2 O N N ? 2 Q N N ? 2 R N N ? 2 T N N ? 2 V N N ? 2 W N N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A NE2 HIS 91 A HIS 167 1_555 F MN MN . A MN 750 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc2 A NE2 HIS 130 A HIS 206 1_555 F MN MN . A MN 750 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc3 A OD2 ASP 131 A ASP 207 1_555 F MN MN . A MN 750 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? metalc ? metalc4 A OD1 ASP 235 A ASP 311 1_555 F MN MN . A MN 750 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc5 A OD2 ASP 235 A ASP 311 1_555 F MN MN . A MN 750 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.737 ? metalc ? metalc6 G O3G T8T . A T8T 800 1_555 I MG MG . A MG 950 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc7 G O2B T8T . A T8T 800 1_555 I MG MG . A MG 950 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.63 ? metalc ? metalc8 H O2B T8T . A T8T 900 1_555 I MG MG . A MG 950 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.67 ? metalc ? metalc9 H O1G T8T . A T8T 900 1_555 I MG MG . A MG 950 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc10 H O2A T8T . A T8T 900 1_555 I MG MG . A MG 950 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc11 I MG MG . A MG 950 1_555 Y O HOH . A HOH 2012 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.917 ? metalc ? metalc12 B NE2 HIS 91 B HIS 167 1_555 K MN MN . B MN 750 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc13 B NE2 HIS 130 B HIS 206 1_555 K MN MN . B MN 750 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc14 B OD2 ASP 131 B ASP 207 1_555 K MN MN . B MN 750 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc15 B OD1 ASP 235 B ASP 311 1_555 K MN MN . B MN 750 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? metalc ? metalc16 B OD2 ASP 235 B ASP 311 1_555 K MN MN . B MN 750 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.587 ? metalc ? metalc17 L O3G T8T . B T8T 800 1_555 N MG MG . B MG 950 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.375 ? metalc ? metalc18 L O2B T8T . B T8T 800 1_555 N MG MG . B MG 950 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.296 ? metalc ? metalc19 M O2A T8T . B T8T 900 1_555 N MG MG . B MG 950 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc20 M O2B T8T . B T8T 900 1_555 N MG MG . B MG 950 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc21 M O1G T8T . B T8T 900 1_555 N MG MG . B MG 950 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.77 ? metalc ? metalc22 C NE2 HIS 91 C HIS 167 1_555 P MN MN . C MN 750 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.164 ? metalc ? metalc23 C NE2 HIS 130 C HIS 206 1_555 P MN MN . C MN 750 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc24 C OD2 ASP 131 C ASP 207 1_555 P MN MN . C MN 750 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc25 C OD2 ASP 235 C ASP 311 1_555 P MN MN . C MN 750 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.631 ? metalc ? metalc26 C OD1 ASP 235 C ASP 311 1_555 P MN MN . C MN 750 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc27 Q O3G T8T . C T8T 800 1_555 S MG MG . C MG 950 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc28 Q O2B T8T . C T8T 800 1_555 S MG MG . C MG 950 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc29 R O2B T8T . C T8T 900 1_555 S MG MG . C MG 950 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? metalc ? metalc30 R O1G T8T . C T8T 900 1_555 S MG MG . C MG 950 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? metalc ? metalc31 R O2A T8T . C T8T 900 1_555 S MG MG . C MG 950 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.278 ? metalc ? metalc32 D NE2 HIS 91 D HIS 167 1_555 U MN MN . D MN 750 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.934 ? metalc ? metalc33 D NE2 HIS 130 D HIS 206 1_555 U MN MN . D MN 750 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc34 D OD2 ASP 131 D ASP 207 1_555 U MN MN . D MN 750 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc35 D OD2 ASP 235 D ASP 311 1_555 U MN MN . D MN 750 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.722 ? metalc ? metalc36 D OD1 ASP 235 D ASP 311 1_555 U MN MN . D MN 750 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.888 ? metalc ? metalc37 V O2B T8T . D T8T 800 1_555 X MG MG . D MG 950 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc38 V O3G T8T . D T8T 800 1_555 X MG MG . D MG 950 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? metalc ? metalc39 W O2A T8T . D T8T 900 1_555 X MG MG . D MG 950 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc40 W O2B T8T . D T8T 900 1_555 X MG MG . D MG 950 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc41 W O1G T8T . D T8T 900 1_555 X MG MG . D MG 950 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.816 ? # _chem_comp.formula 'C10 H16 N5 O12 P3 S' _chem_comp.formula_weight 523.247 _chem_comp.id T8T _chem_comp.mon_nstd_flag . _chem_comp.name "2'-deoxyguanosine-5'-O-(1-thiotriphosphate)" _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 N1 C2 T8T doub 290 n n N1 C6 T8T sing 291 n n N2 C2 T8T sing 292 n n C2 N3 T8T sing 293 n n N2 HN2 T8T sing 294 n n N2 HN2A T8T sing 295 n n N3 C4 T8T sing 296 n n N3 HN3 T8T sing 297 n n C5 C4 T8T doub 298 n y C4 N9 T8T sing 299 n y C6 C5 T8T sing 300 n n C5 N7 T8T sing 301 n y O6 C6 T8T doub 302 n n N7 C8 T8T doub 303 n y N9 C8 T8T sing 304 n y C8 H8 T8T sing 305 n n N9 C1' T8T sing 306 n n S1A PA T8T sing 307 n n PA O5' T8T sing 308 n n PA O2A T8T doub 309 n n PA O3A T8T sing 310 n n O3B PB T8T sing 311 n n O3A PB T8T sing 312 n n PB O1B T8T doub 313 n n PB O2B T8T sing 314 n n O3G PG T8T doub 315 n n O3B PG T8T sing 316 n n PG O1G T8T sing 317 n n PG O2G T8T sing 318 n n O4' C1' T8T sing 319 n n C1' C2' T8T sing 320 n n C1' H1' T8T sing 321 n n S1A HS1A T8T sing 322 n n O1G HO1G T8T sing 323 n n C2' C3' T8T sing 324 n n C2' H2' T8T sing 325 n n C2' "H2'A" T8T sing 326 n n O2B HO2B T8T sing 327 n n O2G HO2G T8T sing 328 n n C4' C3' T8T sing 329 n n C3' O3' T8T sing 330 n n C3' H3' T8T sing 331 n n O3' HO3' T8T sing 332 n n O4' C4' T8T sing 333 n n C4' C5' T8T sing 334 n n C4' H4' T8T sing 335 n n C5' O5' T8T sing 336 n n C5' H5' T8T sing 337 n n C5' "H5'A" T8T sing 338 n n # _atom_sites.entry_id 4BZC _atom_sites.fract_transf_matrix[1][1] 0.012658 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00552 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007208 _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] 0.011641 _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 E 2 T8T A 1 700 700 T8T T8T . F 3 MN A 1 750 750 MN MN . G 2 T8T A 1 800 800 T8T T8T . H 2 T8T A 1 900 900 T8T T8T . I 4 MG A 1 950 950 MG MG . J 2 T8T B 1 700 700 T8T T8T . K 3 MN B 1 750 750 MN MN . L 2 T8T B 1 800 800 T8T T8T . M 2 T8T B 1 900 900 T8T T8T . N 4 MG B 1 950 950 MG MG . O 2 T8T C 1 700 700 T8T T8T . P 3 MN C 1 750 750 MN MN . Q 2 T8T C 1 800 800 T8T T8T . R 2 T8T C 1 900 900 T8T T8T . S 4 MG C 1 950 950 MG MG . T 2 T8T D 1 700 700 T8T T8T . U 3 MN D 1 750 750 MN MN . V 2 T8T D 1 800 800 T8T T8T . W 2 T8T D 1 900 900 T8T T8T . X 4 MG D 1 950 950 MG MG . Y 5 HOH A 1 2001 2001 HOH HOH . Y 5 HOH A 2 2002 2002 HOH HOH . Y 5 HOH A 3 2003 2003 HOH HOH . Y 5 HOH A 4 2004 2004 HOH HOH . Y 5 HOH A 5 2005 2005 HOH HOH . Y 5 HOH A 6 2006 2006 HOH HOH . Y 5 HOH A 7 2007 2007 HOH HOH . Y 5 HOH A 8 2008 2008 HOH HOH . Y 5 HOH A 9 2009 2009 HOH HOH . Y 5 HOH A 10 2010 2010 HOH HOH . Y 5 HOH A 11 2011 2011 HOH HOH . Y 5 HOH A 12 2012 2012 HOH HOH . Y 5 HOH A 13 2013 2013 HOH HOH . Y 5 HOH A 14 2014 2014 HOH HOH . Z 5 HOH B 1 2001 2001 HOH HOH . Z 5 HOH B 2 2002 2002 HOH HOH . Z 5 HOH B 3 2003 2003 HOH HOH . Z 5 HOH B 4 2004 2004 HOH HOH . Z 5 HOH B 5 2005 2005 HOH HOH . Z 5 HOH B 6 2006 2006 HOH HOH . Z 5 HOH B 7 2007 2007 HOH HOH . Z 5 HOH B 8 2008 2008 HOH HOH . Z 5 HOH B 9 2009 2009 HOH HOH . AA 5 HOH C 1 2001 2001 HOH HOH . AA 5 HOH C 2 2002 2002 HOH HOH . AA 5 HOH C 3 2003 2003 HOH HOH . AA 5 HOH C 4 2004 2004 HOH HOH . AA 5 HOH C 5 2005 2005 HOH HOH . AA 5 HOH C 6 2006 2006 HOH HOH . AA 5 HOH C 7 2007 2007 HOH HOH . BA 5 HOH D 1 2001 2001 HOH HOH . BA 5 HOH D 2 2002 2002 HOH HOH . BA 5 HOH D 3 2003 2003 HOH HOH . BA 5 HOH D 4 2004 2004 HOH HOH . # 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 N N1 T8T . . . Q 2 23.348 22.048 17.404 1 32.55 ? N1 T8T 800 C 1 HETATM 2 C C2 T8T . . . Q 2 24.669 22.045 17.093 1 33.09 ? C2 T8T 800 C 1 HETATM 3 N N2 T8T . . . Q 2 25.569 21.728 18.066 1 34.27 ? N2 T8T 800 C 1 HETATM 4 N N3 T8T . . . Q 2 25.16 22.295 15.863 1 32.01 ? N3 T8T 800 C 1 HETATM 5 C C4 T8T . . . Q 2 24.274 22.587 14.904 1 32.01 ? C4 T8T 800 C 1 HETATM 6 C C5 T8T . . . Q 2 22.832 22.641 15.166 1 32.22 ? C5 T8T 800 C 1 HETATM 7 C C6 T8T . . . Q 2 22.392 22.341 16.519 1 32.3 ? C6 T8T 800 C 1 HETATM 8 O O6 T8T . . . Q 2 21.165 22.41 16.785 1 32.26 ? O6 T8T 800 C 1 HETATM 9 N N7 T8T . . . Q 2 22.202 22.99 14.037 1 31.94 ? N7 T8T 800 C 1 HETATM 10 C C8 T8T . . . Q 2 23.166 23.146 13.117 1 32.05 ? C8 T8T 800 C 1 HETATM 11 N N9 T8T . . . Q 2 24.386 22.899 13.638 1 31.87 ? N9 T8T 800 C 1 HETATM 12 P PA T8T . . . Q 2 22.779 25.991 10.741 1 32.3 ? PA T8T 800 C 1 HETATM 13 P PB T8T . . . Q 2 22.231 27.101 8.187 1 34.34 ? PB T8T 800 C 1 HETATM 14 P PG T8T . . . Q 2 20.742 29.535 8.138 1 36.33 ? PG T8T 800 C 1 HETATM 15 C C1' T8T . . . Q 2 25.709 23.009 12.998 1 31.45 ? C1' T8T 800 C 1 HETATM 16 S S1A T8T . . . Q 2 22.454 27.344 12.004 1 31.61 ? S1A T8T 800 C 1 HETATM 17 O O1B T8T . . . Q 2 21.417 25.896 7.755 1 34.16 ? O1B T8T 800 C 1 HETATM 18 O O1G T8T . . . Q 2 21.528 30.718 8.64 1 35.23 ? O1G T8T 800 C 1 HETATM 19 C C2' T8T . . . Q 2 25.681 22.69 11.519 1 31.26 ? C2' T8T 800 C 1 HETATM 20 O O2A T8T . . . Q 2 21.577 25.146 10.556 1 31.45 ? O2A T8T 800 C 1 HETATM 21 O O2B T8T . . . Q 2 23.171 27.578 7.104 1 35.29 ? O2B T8T 800 C 1 HETATM 22 O O2G T8T . . . Q 2 19.267 29.592 8.448 1 36.41 ? O2G T8T 800 C 1 HETATM 23 C C3' T8T . . . Q 2 26.554 23.778 11.02 1 31.38 ? C3' T8T 800 C 1 HETATM 24 O O3' T8T . . . Q 2 27.843 23.239 11.12 1 31.36 ? O3' T8T 800 C 1 HETATM 25 O O3A T8T . . . Q 2 23.224 26.779 9.399 1 33.5 ? O3A T8T 800 C 1 HETATM 26 O O3B T8T . . . Q 2 21.314 28.225 8.912 1 34.22 ? O3B T8T 800 C 1 HETATM 27 O O3G T8T . . . Q 2 20.974 29.304 6.651 1 37.46 ? O3G T8T 800 C 1 HETATM 28 C C4' T8T . . . Q 2 26.421 24.945 11.971 1 31.19 ? C4' T8T 800 C 1 HETATM 29 O O4' T8T . . . Q 2 26.14 24.365 13.221 1 30.66 ? O4' T8T 800 C 1 HETATM 30 C C5' T8T . . . Q 2 25.324 25.922 11.57 1 31.26 ? C5' T8T 800 C 1 HETATM 31 O O5' T8T . . . Q 2 24.139 25.224 11.166 1 31.72 ? O5' T8T 800 C 1 # _model_server_stats.io_time_ms 40 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 52 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 31 #