data_6UPA # _model_server_result.job_id iyK00_rKZb1mMJytCDO7ow _model_server_result.datetime_utc '2024-10-20 09:22:47' _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 6upa # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 6UPA # _exptl.entry_id 6UPA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.18 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-TRIPHOSPHATE" _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 90 _cell.entry_id 6UPA _cell.length_a 82.73 _cell.length_b 82.73 _cell.length_c 170.35 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6UPA _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 disulf ? disulf1 B SG CYS 78 A CYS 111 1_555 B SG CYS 81 A CYS 114 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.032 ? metalc ? metalc1 A OG SER 31 B SER 56 1_555 D MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc2 C O3G GTP . B GTP 401 1_555 D MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? metalc ? metalc3 C O1B GTP . B GTP 401 1_555 D MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.109 ? metalc ? metalc4 D MG MG . B MG 402 1_555 F O HOH . B HOH 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.931 ? metalc ? metalc5 D MG MG . B MG 402 1_555 F O HOH . B HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc6 D MG MG . B MG 402 1_555 F O HOH . B HOH 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? # _chem_comp.formula 'C10 H16 N5 O14 P3' _chem_comp.formula_weight 523.18 _chem_comp.id GTP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-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 GTP doub 174 n n PG O2G GTP sing 175 n n PG O3G GTP sing 176 n n PG O3B GTP sing 177 n n O2G HOG2 GTP sing 178 n n O3G HOG3 GTP sing 179 n n O3B PB GTP sing 180 n n PB O1B GTP doub 181 n n PB O2B GTP sing 182 n n PB O3A GTP sing 183 n n O2B HOB2 GTP sing 184 n n O3A PA GTP sing 185 n n PA O1A GTP doub 186 n n PA O2A GTP sing 187 n n PA O5' GTP sing 188 n n O2A HOA2 GTP sing 189 n n O5' C5' GTP sing 190 n n C5' C4' GTP sing 191 n n C5' H5' GTP sing 192 n n C5' "H5''" GTP sing 193 n n C4' O4' GTP sing 194 n n C4' C3' GTP sing 195 n n C4' H4' GTP sing 196 n n O4' C1' GTP sing 197 n n C3' O3' GTP sing 198 n n C3' C2' GTP sing 199 n n C3' H3' GTP sing 200 n n O3' HO3' GTP sing 201 n n C2' O2' GTP sing 202 n n C2' C1' GTP sing 203 n n C2' H2' GTP sing 204 n n O2' HO2' GTP sing 205 n n C1' N9 GTP sing 206 n n C1' H1' GTP sing 207 n n N9 C8 GTP sing 208 n y N9 C4 GTP sing 209 n y C8 N7 GTP doub 210 n y C8 H8 GTP sing 211 n n N7 C5 GTP sing 212 n y C5 C6 GTP sing 213 n n C5 C4 GTP doub 214 n y C6 O6 GTP doub 215 n n C6 N1 GTP sing 216 n n N1 C2 GTP sing 217 n n N1 HN1 GTP sing 218 n n C2 N2 GTP sing 219 n n C2 N3 GTP doub 220 n n N2 HN21 GTP sing 221 n n N2 HN22 GTP sing 222 n n N3 C4 GTP sing 223 n n # _atom_sites.entry_id 6UPA _atom_sites.fract_transf_matrix[1][1] 0.012088 _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] 0.012088 _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] 0.00587 _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 C 3 GTP B 1 401 500 GTP GTP . D 4 MG B 1 402 1 MG MG . E 5 GDP A 1 1401 1401 GDP GDP . F 6 HOH B 1 501 24 HOH HOH . F 6 HOH B 2 502 21 HOH HOH . F 6 HOH B 3 503 23 HOH HOH . F 6 HOH B 4 504 29 HOH HOH . F 6 HOH B 5 505 4 HOH HOH . F 6 HOH B 6 506 1 HOH HOH . F 6 HOH B 7 507 17 HOH HOH . F 6 HOH B 8 508 15 HOH HOH . F 6 HOH B 9 509 5 HOH HOH . F 6 HOH B 10 510 18 HOH HOH . F 6 HOH B 11 511 16 HOH HOH . F 6 HOH B 12 512 11 HOH HOH . F 6 HOH B 13 513 6 HOH HOH . F 6 HOH B 14 514 12 HOH HOH . F 6 HOH B 15 515 2 HOH HOH . F 6 HOH B 16 516 8 HOH HOH . F 6 HOH B 17 517 7 HOH HOH . G 6 HOH A 1 1501 25 HOH HOH . G 6 HOH A 2 1502 20 HOH HOH . G 6 HOH A 3 1503 27 HOH HOH . G 6 HOH A 4 1504 30 HOH HOH . G 6 HOH A 5 1505 9 HOH HOH . G 6 HOH A 6 1506 3 HOH HOH . G 6 HOH A 7 1507 26 HOH HOH . G 6 HOH A 8 1508 14 HOH HOH . G 6 HOH A 9 1509 32 HOH HOH . G 6 HOH A 10 1510 13 HOH HOH . G 6 HOH A 11 1511 10 HOH HOH . G 6 HOH A 12 1512 19 HOH HOH . G 6 HOH A 13 1513 22 HOH HOH . G 6 HOH A 14 1514 28 HOH HOH . G 6 HOH A 15 1515 31 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 GTP . . . C 3 4.547 28.192 -12.29 1 59.32 ? PG GTP 401 B 1 HETATM 2 O O1G GTP . . . C 3 4.204 28.246 -13.762 1 54.53 ? O1G GTP 401 B 1 HETATM 3 O O2G GTP . . . C 3 5.745 29.066 -12.018 1 64.28 ? O2G GTP 401 B 1 HETATM 4 O O3G GTP . . . C 3 4.875 26.773 -11.895 1 59.8 ? O3G GTP 401 B 1 HETATM 5 O O3B GTP . . . C 3 3.273 28.746 -11.473 1 62.34 ? O3B GTP 401 B 1 HETATM 6 P PB GTP . . . C 3 1.975 27.83 -11.22 1 75.18 ? PB GTP 401 B 1 HETATM 7 O O1B GTP . . . C 3 2.415 26.464 -10.759 1 55.67 ? O1B GTP 401 B 1 HETATM 8 O O2B GTP . . . C 3 1.127 27.713 -12.462 1 68.7 ? O2B GTP 401 B 1 HETATM 9 O O3A GTP . . . C 3 1.152 28.57 -10.043 1 64.22 ? O3A GTP 401 B 1 HETATM 10 P PA GTP . . . C 3 1.361 28.224 -8.48 1 59.28 ? PA GTP 401 B 1 HETATM 11 O O1A GTP . . . C 3 2.816 28.391 -8.12 1 50.2 ? O1A GTP 401 B 1 HETATM 12 O O2A GTP . . . C 3 0.867 26.833 -8.162 1 72.34 ? O2A GTP 401 B 1 HETATM 13 O O5' GTP . . . C 3 0.493 29.315 -7.679 1 48.1 ? O5' GTP 401 B 1 HETATM 14 C C5' GTP . . . C 3 0.421 30.666 -8.067 1 46.95 ? C5' GTP 401 B 1 HETATM 15 C C4' GTP . . . C 3 -0.203 31.463 -6.926 1 47.23 ? C4' GTP 401 B 1 HETATM 16 O O4' GTP . . . C 3 -1.563 31.707 -7.22 1 46.11 ? O4' GTP 401 B 1 HETATM 17 C C3' GTP . . . C 3 -0.179 30.686 -5.619 1 50.2 ? C3' GTP 401 B 1 HETATM 18 O O3' GTP . . . C 3 0.851 31.157 -4.787 1 43.17 ? O3' GTP 401 B 1 HETATM 19 C C2' GTP . . . C 3 -1.515 30.969 -4.973 1 53.58 ? C2' GTP 401 B 1 HETATM 20 O O2' GTP . . . C 3 -1.337 31.941 -3.973 1 47.22 ? O2' GTP 401 B 1 HETATM 21 C C1' GTP . . . C 3 -2.387 31.535 -6.083 1 51.59 ? C1' GTP 401 B 1 HETATM 22 N N9 GTP . . . C 3 -3.475 30.599 -6.425 1 47.01 ? N9 GTP 401 B 1 HETATM 23 C C8 GTP . . . C 3 -3.371 29.236 -6.524 1 44.93 ? C8 GTP 401 B 1 HETATM 24 N N7 GTP . . . C 3 -4.582 28.735 -6.863 1 43.35 ? N7 GTP 401 B 1 HETATM 25 C C5 GTP . . . C 3 -5.453 29.758 -6.984 1 42.59 ? C5 GTP 401 B 1 HETATM 26 C C6 GTP . . . C 3 -6.802 29.801 -7.308 1 48.73 ? C6 GTP 401 B 1 HETATM 27 O O6 GTP . . . C 3 -7.413 28.762 -7.551 1 43.98 ? O6 GTP 401 B 1 HETATM 28 N N1 GTP . . . C 3 -7.451 31.017 -7.358 1 55.4 ? N1 GTP 401 B 1 HETATM 29 C C2 GTP . . . C 3 -6.758 32.178 -7.084 1 46.62 ? C2 GTP 401 B 1 HETATM 30 N N2 GTP . . . C 3 -7.384 33.349 -7.13 1 54.64 ? N2 GTP 401 B 1 HETATM 31 N N3 GTP . . . C 3 -5.417 32.127 -6.761 1 42.82 ? N3 GTP 401 B 1 HETATM 32 C C4 GTP . . . C 3 -4.773 30.936 -6.711 1 44.11 ? C4 GTP 401 B 1 # _model_server_stats.io_time_ms 35 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 22 _model_server_stats.element_count 32 #