data_5HRF # _model_server_result.job_id LXdLSUS8DpekVOY6_VWodg _model_server_result.datetime_utc '2025-01-06 23:04:06' _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 5hrf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":202}' # _entry.id 5HRF # _exptl.entry_id 5HRF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYGUANOSINE-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 90 _cell.entry_id 5HRF _cell.length_a 58.706 _cell.length_b 75.441 _cell.length_c 108.45 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5HRF _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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 _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 I 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 OD1 ASP 53 A ASP 49 1_555 E MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc2 A OD2 ASP 55 A ASP 51 1_555 E MN MN . A MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc3 E MN MN . A MN 201 1_555 F O1G DGT . A DGT 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc4 E MN MN . A MN 201 1_555 F O2B DGT . A DGT 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? metalc ? metalc5 E MN MN . A MN 201 1_555 F O2A DGT . A DGT 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc6 E MN MN . A MN 201 1_555 K O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? metalc ? metalc7 B OD1 ASP 53 B ASP 49 1_555 G MN MN . B MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? metalc ? metalc8 B OD2 ASP 55 B ASP 51 1_555 G MN MN . B MN 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc9 G MN MN . B MN 201 1_555 I O3G DGT . B DGT 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? metalc ? metalc10 G MN MN . B MN 201 1_555 I O1A DGT . B DGT 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc11 G MN MN . B MN 201 1_555 I O2B DGT . B DGT 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc12 G MN MN . B MN 201 1_555 L O HOH . B HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? hydrog WATSON-CRICK hydrog1 C N1 DA 2 C DA 2 1_555 D N3 DT 9 D DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 C N6 DA 2 C DA 2 1_555 D O4 DT 9 D DT 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 C N1 DG 3 C DG 3 1_555 D N3 DC 8 D DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 C N2 DG 3 C DG 3 1_555 D O2 DC 8 D DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 C O6 DG 3 C DG 3 1_555 D N4 DC 8 D DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 C N1 DG 4 C DG 4 1_555 D N3 DC 7 D DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 C N2 DG 4 C DG 4 1_555 D O2 DC 7 D DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 C O6 DG 4 C DG 4 1_555 D N4 DC 7 D DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 C N1 DA 5 C DA 5 1_555 D N3 DT 6 D DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 C N6 DA 5 C DA 5 1_555 D O4 DT 6 D DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 C N3 DT 6 C DT 6 1_555 D N1 DA 5 D DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 C O4 DT 6 C DT 6 1_555 D N6 DA 5 D DA 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 C N3 DC 7 C DC 7 1_555 D N1 DG 4 D DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 C N4 DC 7 C DC 7 1_555 D O6 DG 4 D DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 C O2 DC 7 C DC 7 1_555 D N2 DG 4 D DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 C N3 DC 8 C DC 8 1_555 D N1 DG 3 D DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 C N4 DC 8 C DC 8 1_555 D O6 DG 3 D DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 C O2 DC 8 C DC 8 1_555 D N2 DG 3 D DG 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 C N3 DT 9 C DT 9 1_555 D N1 DA 2 D DA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 C O4 DT 9 C DT 9 1_555 D N6 DA 2 D DA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id DGT _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYGUANOSINE-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 DGT sing 195 n n PG O2G DGT sing 196 n n O1G HO1G DGT sing 197 n n O2G HO2G DGT sing 198 n n O3G PG DGT doub 199 n n O3B PG DGT sing 200 n n PB O3B DGT sing 201 n n PB O1B DGT sing 202 n n PB O3A DGT sing 203 n n O1B HO1B DGT sing 204 n n O2B PB DGT doub 205 n n PA O3A DGT sing 206 n n PA O1A DGT sing 207 n n O1A HO1A DGT sing 208 n n O2A PA DGT doub 209 n n O5' PA DGT sing 210 n n O5' C5' DGT sing 211 n n C5' H5' DGT sing 212 n n C5' "H5'A" DGT sing 213 n n C4' C5' DGT sing 214 n n C4' H4' DGT sing 215 n n O4' C4' DGT sing 216 n n C3' C4' DGT sing 217 n n C3' O3' DGT sing 218 n n C3' H3' DGT sing 219 n n O3' HO3' DGT sing 220 n n C2' C3' DGT sing 221 n n C2' C1' DGT sing 222 n n C2' H2' DGT sing 223 n n C2' "H2'A" DGT sing 224 n n C1' O4' DGT sing 225 n n C1' H1' DGT sing 226 n n N9 C1' DGT sing 227 n n N9 C4 DGT sing 228 n y C8 N9 DGT sing 229 n y C8 H8 DGT sing 230 n n N7 C8 DGT doub 231 n y N7 C5 DGT sing 232 n y C5 C6 DGT sing 233 n n C5 C4 DGT doub 234 n y C6 N1 DGT sing 235 n n O6 C6 DGT doub 236 n n N1 C2 DGT sing 237 n n C2 N3 DGT doub 238 n n C2 N2 DGT sing 239 n n N2 HN2 DGT sing 240 n n N2 HN2A DGT sing 241 n n C4 N3 DGT sing 242 n n N1 H16 DGT sing 243 n n # _atom_sites.entry_id 5HRF _atom_sites.fract_transf_matrix[1][1] 0.017034 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013255 _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] 0.009221 _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 3 MN A 1 201 1 MN MN . F 4 DGT A 1 202 11 DGT GTP . G 3 MN B 1 201 2 MN MN . H 5 SO4 B 1 202 1 SO4 SO4 . I 4 DGT B 1 203 11 DGT GTP . J 5 SO4 D 1 101 2 SO4 SO4 . K 6 HOH A 1 301 36 HOH HOH . K 6 HOH A 2 302 1 HOH HOH . K 6 HOH A 3 303 41 HOH HOH . K 6 HOH A 4 304 57 HOH HOH . K 6 HOH A 5 305 34 HOH HOH . K 6 HOH A 6 306 19 HOH HOH . K 6 HOH A 7 307 38 HOH HOH . K 6 HOH A 8 308 32 HOH HOH . K 6 HOH A 9 309 28 HOH HOH . K 6 HOH A 10 310 20 HOH HOH . K 6 HOH A 11 311 18 HOH HOH . K 6 HOH A 12 312 56 HOH HOH . K 6 HOH A 13 313 16 HOH HOH . K 6 HOH A 14 314 4 HOH HOH . K 6 HOH A 15 315 5 HOH HOH . K 6 HOH A 16 316 60 HOH HOH . K 6 HOH A 17 317 39 HOH HOH . K 6 HOH A 18 318 76 HOH HOH . K 6 HOH A 19 319 8 HOH HOH . K 6 HOH A 20 320 9 HOH HOH . K 6 HOH A 21 321 77 HOH HOH . K 6 HOH A 22 322 25 HOH HOH . K 6 HOH A 23 323 58 HOH HOH . K 6 HOH A 24 324 75 HOH HOH . K 6 HOH A 25 325 64 HOH HOH . K 6 HOH A 26 326 23 HOH HOH . K 6 HOH A 27 327 13 HOH HOH . K 6 HOH A 28 328 65 HOH HOH . K 6 HOH A 29 329 68 HOH HOH . K 6 HOH A 30 330 55 HOH HOH . K 6 HOH A 31 331 37 HOH HOH . K 6 HOH A 32 332 21 HOH HOH . K 6 HOH A 33 333 54 HOH HOH . K 6 HOH A 34 334 73 HOH HOH . K 6 HOH A 35 335 10 HOH HOH . K 6 HOH A 36 336 33 HOH HOH . K 6 HOH A 37 337 72 HOH HOH . K 6 HOH A 38 338 71 HOH HOH . K 6 HOH A 39 339 40 HOH HOH . L 6 HOH B 1 301 2 HOH HOH . L 6 HOH B 2 302 27 HOH HOH . L 6 HOH B 3 303 44 HOH HOH . L 6 HOH B 4 304 12 HOH HOH . L 6 HOH B 5 305 78 HOH HOH . L 6 HOH B 6 306 26 HOH HOH . L 6 HOH B 7 307 14 HOH HOH . L 6 HOH B 8 308 43 HOH HOH . L 6 HOH B 9 309 6 HOH HOH . L 6 HOH B 10 310 7 HOH HOH . L 6 HOH B 11 311 80 HOH HOH . L 6 HOH B 12 312 67 HOH HOH . L 6 HOH B 13 313 45 HOH HOH . L 6 HOH B 14 314 35 HOH HOH . L 6 HOH B 15 315 66 HOH HOH . L 6 HOH B 16 316 79 HOH HOH . L 6 HOH B 17 317 22 HOH HOH . L 6 HOH B 18 318 46 HOH HOH . L 6 HOH B 19 319 42 HOH HOH . L 6 HOH B 20 320 47 HOH HOH . L 6 HOH B 21 321 11 HOH HOH . M 6 HOH C 1 101 24 HOH HOH . M 6 HOH C 2 102 50 HOH HOH . M 6 HOH C 3 103 29 HOH HOH . M 6 HOH C 4 104 62 HOH HOH . M 6 HOH C 5 105 3 HOH HOH . M 6 HOH C 6 106 59 HOH HOH . M 6 HOH C 7 107 49 HOH HOH . M 6 HOH C 8 108 74 HOH HOH . N 6 HOH D 1 201 70 HOH HOH . N 6 HOH D 2 202 61 HOH HOH . N 6 HOH D 3 203 52 HOH HOH . N 6 HOH D 4 204 48 HOH HOH . N 6 HOH D 5 205 31 HOH HOH . N 6 HOH D 6 206 51 HOH HOH . N 6 HOH D 7 207 63 HOH HOH . N 6 HOH D 8 208 30 HOH HOH . N 6 HOH D 9 209 53 HOH HOH . N 6 HOH D 10 210 81 HOH HOH . N 6 HOH D 11 211 69 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 P PG DGT . . . F 4 28.962 21.646 -2.715 1 36.33 ? PG DGT 202 A 1 HETATM 2 O O1G DGT . . . F 4 28.31 20.558 -1.901 1 41.59 ? O1G DGT 202 A 1 HETATM 3 O O2G DGT . . . F 4 30.384 21.945 -2.3 1 39.39 ? O2G DGT 202 A 1 HETATM 4 O O3G DGT . . . F 4 28.723 21.442 -4.175 1 34.85 ? O3G DGT 202 A 1 HETATM 5 O O3B DGT . . . F 4 28.23 23.052 -2.417 1 35.63 ? O3B DGT 202 A 1 HETATM 6 P PB DGT . . . F 4 27.198 23.292 -1.198 1 36.51 ? PB DGT 202 A 1 HETATM 7 O O1B DGT . . . F 4 26.76 24.727 -1.219 1 35.21 ? O1B DGT 202 A 1 HETATM 8 O O2B DGT . . . F 4 26.24 22.151 -1.253 1 41.54 ? O2B DGT 202 A 1 HETATM 9 O O3A DGT . . . F 4 28.092 23.181 0.117 1 37.02 ? O3A DGT 202 A 1 HETATM 10 P PA DGT . . . F 4 27.969 22.098 1.297 1 37.94 ? PA DGT 202 A 1 HETATM 11 O O1A DGT . . . F 4 29.355 22.135 1.879 1 39.44 ? O1A DGT 202 A 1 HETATM 12 O O2A DGT . . . F 4 27.398 20.802 0.807 1 43.1 ? O2A DGT 202 A 1 HETATM 13 O O5' DGT . . . F 4 26.978 22.809 2.333 1 37.48 ? O5' DGT 202 A 1 HETATM 14 C C5' DGT . . . F 4 25.571 22.675 2.214 1 37.38 ? C5' DGT 202 A 1 HETATM 15 C C4' DGT . . . F 4 24.929 23.892 2.851 1 36.72 ? C4' DGT 202 A 1 HETATM 16 O O4' DGT . . . F 4 25.316 24.018 4.211 1 36.57 ? O4' DGT 202 A 1 HETATM 17 C C3' DGT . . . F 4 25.366 25.195 2.223 1 35.46 ? C3' DGT 202 A 1 HETATM 18 O O3' DGT . . . F 4 24.717 25.453 0.979 1 34.65 ? O3' DGT 202 A 1 HETATM 19 C C2' DGT . . . F 4 25.025 26.177 3.316 1 36.42 ? C2' DGT 202 A 1 HETATM 20 C C1' DGT . . . F 4 25.419 25.397 4.561 1 36.53 ? C1' DGT 202 A 1 HETATM 21 N N9 DGT . . . F 4 26.818 25.755 4.953 1 37.35 ? N9 DGT 202 A 1 HETATM 22 C C8 DGT . . . F 4 27.96 25.145 4.554 1 38.58 ? C8 DGT 202 A 1 HETATM 23 N N7 DGT . . . F 4 29.058 25.741 5.094 1 39.42 ? N7 DGT 202 A 1 HETATM 24 C C5 DGT . . . F 4 28.615 26.756 5.85 1 37.38 ? C5 DGT 202 A 1 HETATM 25 C C6 DGT . . . F 4 29.23 27.793 6.692 1 37.26 ? C6 DGT 202 A 1 HETATM 26 O O6 DGT . . . F 4 30.463 27.853 6.818 1 44.88 ? O6 DGT 202 A 1 HETATM 27 N N1 DGT . . . F 4 28.43 28.667 7.31 1 38.3 ? N1 DGT 202 A 1 HETATM 28 C C2 DGT . . . F 4 27.085 28.631 7.18 1 38.04 ? C2 DGT 202 A 1 HETATM 29 N N2 DGT . . . F 4 26.319 29.542 7.833 1 39.28 ? N2 DGT 202 A 1 HETATM 30 N N3 DGT . . . F 4 26.453 27.703 6.43 1 37.81 ? N3 DGT 202 A 1 HETATM 31 C C4 DGT . . . F 4 27.15 26.765 5.75 1 37.1 ? C4 DGT 202 A 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 247 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #