data_4BZC # _model_server_result.job_id oUhP2lGysj_YNG8YT45Ewg _model_server_result.datetime_utc '2024-11-07 02:51:26' _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":"O","auth_seq_id":700}' # _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 . . . O 2 19.726 11.257 7.322 1 46.75 ? N1 T8T 700 C 1 HETATM 2 C C2 T8T . . . O 2 20.954 11.079 7.802 1 45.32 ? C2 T8T 700 C 1 HETATM 3 N N2 T8T . . . O 2 21.913 11.957 7.5 1 47.47 ? N2 T8T 700 C 1 HETATM 4 N N3 T8T . . . O 2 21.33 10.07 8.568 1 43.76 ? N3 T8T 700 C 1 HETATM 5 C C4 T8T . . . O 2 20.425 9.176 8.927 1 45.3 ? C4 T8T 700 C 1 HETATM 6 C C5 T8T . . . O 2 19.055 9.273 8.471 1 48.04 ? C5 T8T 700 C 1 HETATM 7 C C6 T8T . . . O 2 18.742 10.409 7.612 1 50.66 ? C6 T8T 700 C 1 HETATM 8 O O6 T8T . . . O 2 17.556 10.534 7.209 1 59.57 ? O6 T8T 700 C 1 HETATM 9 N N7 T8T . . . O 2 18.36 8.261 8.974 1 47.09 ? N7 T8T 700 C 1 HETATM 10 C C8 T8T . . . O 2 19.265 7.554 9.688 1 47.18 ? C8 T8T 700 C 1 HETATM 11 N N9 T8T . . . O 2 20.481 8.129 9.68 1 45.23 ? N9 T8T 700 C 1 HETATM 12 P PA T8T . . . O 2 20.337 3.434 10.26 1 49.98 ? PA T8T 700 C 1 HETATM 13 P PB T8T . . . O 2 18.163 2.258 11.617 1 45.44 ? PB T8T 700 C 1 HETATM 14 P PG T8T . . . O 2 16.991 3.174 14.016 1 47.88 ? PG T8T 700 C 1 HETATM 15 C C1' T8T . . . O 2 21.75 7.696 10.304 1 45.44 ? C1' T8T 700 C 1 HETATM 16 S S1A T8T . . . O 2 21.255 1.799 10.644 1 49.7 ? S1A T8T 700 C 1 HETATM 17 O O1B T8T . . . O 2 17.025 1.622 10.832 1 43.73 ? O1B T8T 700 C 1 HETATM 18 O O1G T8T . . . O 2 17.558 1.799 14.428 1 47.59 ? O1G T8T 700 C 1 HETATM 19 C C2' T8T . . . O 2 21.964 8.298 11.685 1 44.8 ? C2' T8T 700 C 1 HETATM 20 O O2A T8T . . . O 2 20.525 4.259 9.046 1 53.52 ? O2A T8T 700 C 1 HETATM 21 O O2B T8T . . . O 2 19.265 1.421 12.224 1 47.74 ? O2B T8T 700 C 1 HETATM 22 O O2G T8T . . . O 2 15.555 3.253 13.529 1 46.83 ? O2G T8T 700 C 1 HETATM 23 C C3' T8T . . . O 2 22.35 7.143 12.576 1 44.02 ? C3' T8T 700 C 1 HETATM 24 O O3' T8T . . . O 2 23.757 7.166 12.762 1 42.81 ? O3' T8T 700 C 1 HETATM 25 O O3A T8T . . . O 2 18.773 3.316 10.563 1 51.75 ? O3A T8T 700 C 1 HETATM 26 O O3B T8T . . . O 2 17.831 3.429 12.656 1 46.61 ? O3B T8T 700 C 1 HETATM 27 O O3G T8T . . . O 2 17.27 4.335 14.916 1 43.61 ? O3G T8T 700 C 1 HETATM 28 C C4' T8T . . . O 2 21.935 5.924 11.801 1 45.49 ? C4' T8T 700 C 1 HETATM 29 O O4' T8T . . . O 2 21.734 6.282 10.442 1 46.49 ? O4' T8T 700 C 1 HETATM 30 C C5' T8T . . . O 2 20.596 5.351 12.165 1 47.4 ? C5' T8T 700 C 1 HETATM 31 O O5' T8T . . . O 2 20.746 4.028 11.678 1 51.89 ? O5' T8T 700 C 1 # _model_server_stats.io_time_ms 233 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 209 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #