data_5SVQ # _model_server_result.job_id 8IntTw0YVo5WAZsxVEHF0A _model_server_result.datetime_utc '2024-11-23 08:28:48' _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 5svq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":406}' # _entry.id 5SVQ # _exptl.entry_id 5SVQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 718.27 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "SPIRO(2,4,6-TRINITROBENZENE[1,2A]-2O',3O'-METHYLENE-ADENINE-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 120 _cell.entry_id 5SVQ _cell.length_a 120.45 _cell.length_b 120.45 _cell.length_c 235.99 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5SVQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id G _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 A SG CYS 106 A CYS 107 1_555 A SG CYS 152 A CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 115 A CYS 116 1_555 A SG CYS 136 A CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 A SG CYS 121 A CYS 122 1_555 A SG CYS 146 A CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 202 A CYS 203 1_555 A SG CYS 212 A CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf5 A SG CYS 246 A CYS 247 1_555 A SG CYS 255 A CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? covale ? covale1 A ND2 ASN 169 A ASN 170 1_555 B C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.419 ? covale ? covale2 A ND2 ASN 193 A ASN 194 1_555 C C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.427 ? covale ? covale3 A ND2 ASN 289 A ASN 290 1_555 D C1 NAG . A NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? # _chem_comp.formula 'C16 H17 N8 O19 P3' _chem_comp.formula_weight 718.27 _chem_comp.id 128 _chem_comp.mon_nstd_flag . _chem_comp.name "SPIRO(2,4,6-TRINITROBENZENE[1,2A]-2O',3O'-METHYLENE-ADENINE-TRIPHOSPHATE" _chem_comp.type 'rna linking' _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 128 doub 1 n n PG O2G 128 sing 2 n n PG O3G 128 sing 3 n n PG O3B 128 sing 4 n n O2G HOG2 128 sing 5 n n O3G HOG3 128 sing 6 n n PB O1B 128 doub 7 n n PB O2B 128 sing 8 n n PB O3B 128 sing 9 n n PB O3A 128 sing 10 n n O2B HOB2 128 sing 11 n n PA O1A 128 doub 12 n n PA O2A 128 sing 13 n n PA O3A 128 sing 14 n n PA O5' 128 sing 15 n n O2A HOA2 128 sing 16 n n O5' C5' 128 sing 17 n n C5' C4' 128 sing 18 n n C5' H5' 128 sing 19 n n C5' "H5''" 128 sing 20 n n C4' O4' 128 sing 21 n n C4' C3' 128 sing 22 n n C4' H4' 128 sing 23 n n O4' C1' 128 sing 24 n n C3' O3' 128 sing 25 n n C3' C2' 128 sing 26 n n C3' H3' 128 sing 27 n n O3' C1F 128 sing 28 n n C2' O2' 128 sing 29 n n C2' C1' 128 sing 30 n n C2' H2' 128 sing 31 n n O2' C1F 128 sing 32 n n C1' N9 128 sing 33 n n C1' H1' 128 sing 34 n n N9 C8 128 sing 35 n y N9 C4 128 sing 36 n y C8 N7 128 doub 37 n y C8 H8 128 sing 38 n n N7 C5 128 sing 39 n y C5 C6 128 sing 40 n y C5 C4 128 doub 41 n y C6 N6 128 sing 42 n n C6 N1 128 doub 43 n y N6 HN61 128 sing 44 n n N6 HN62 128 sing 45 n n N1 C2 128 sing 46 n y C2 N3 128 doub 47 n y C2 H2 128 sing 48 n n N3 C4 128 sing 49 n y C1F C2F 128 sing 50 n n C1F C6F 128 sing 51 n n C2F C3F 128 doub 52 n n C2F N2F 128 sing 53 n n C3F C4F 128 sing 54 n n C3F H3F 128 sing 55 n n C4F C5F 128 sing 56 n n C4F N4F 128 doub 57 n n O4F H4F 128 sing 58 n n C5F C6F 128 doub 59 n n C5F H5F 128 sing 60 n n C6F N6F 128 sing 61 n n N2F O2F 128 doub 62 n n N2F O3F 128 sing 63 n n N4F O4F 128 sing 64 n n N4F O5F 128 sing 65 n n N6F O6F 128 doub 66 n n N6F O7F 128 sing 67 n n # _atom_sites.entry_id 5SVQ _atom_sites.fract_transf_matrix[1][1] 0.008302 _atom_sites.fract_transf_matrix[1][2] 0.004793 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009587 _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] 0.004237 _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 NAG A 1 401 500 NAG NAG . C 2 NAG A 1 402 501 NAG NAG . D 2 NAG A 1 403 502 NAG NAG . E 3 NA A 1 404 1 NA NA . F 4 MG A 1 405 1 MG MG . G 5 128 A 1 406 1 128 LIG . H 6 HOH A 1 501 1 HOH HOH . H 6 HOH A 2 502 2 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 128 . . . G 5 14.822 -14.476 -33.029 1 176.55 ? PG 128 406 A 1 HETATM 2 O O1G 128 . . . G 5 15.227 -15.782 -33.641 1 160.7 ? O1G 128 406 A 1 HETATM 3 O O2G 128 . . . G 5 14.683 -13.347 -34.052 1 167.93 ? O2G 128 406 A 1 HETATM 4 O O3G 128 . . . G 5 13.514 -14.561 -32.251 1 175.87 ? O3G 128 406 A 1 HETATM 5 P PB 128 . . . G 5 17.456 -14.342 -31.815 1 169.46 ? PB 128 406 A 1 HETATM 6 O O1B 128 . . . G 5 18.256 -13.095 -31.765 1 140.96 ? O1B 128 406 A 1 HETATM 7 O O2B 128 . . . G 5 17.654 -15.181 -30.543 1 140.83 ? O2B 128 406 A 1 HETATM 8 O O3B 128 . . . G 5 15.91 -13.994 -31.97 1 164.64 ? O3B 128 406 A 1 HETATM 9 P PA 128 . . . G 5 18.274 -14.801 -34.579 1 201.24 ? PA 128 406 A 1 HETATM 10 O O1A 128 . . . G 5 19.132 -15.851 -35.178 1 170.99 ? O1A 128 406 A 1 HETATM 11 O O2A 128 . . . G 5 19.057 -13.481 -34.525 1 178.04 ? O2A 128 406 A 1 HETATM 12 O O3A 128 . . . G 5 17.868 -15.203 -33.09 1 176.73 ? O3A 128 406 A 1 HETATM 13 O O5' 128 . . . G 5 16.945 -14.562 -35.415 1 188.58 ? O5' 128 406 A 1 HETATM 14 C C5' 128 . . . G 5 16.803 -14.822 -36.827 1 169.04 ? C5' 128 406 A 1 HETATM 15 C C4' 128 . . . G 5 15.766 -13.887 -37.391 1 160.77 ? C4' 128 406 A 1 HETATM 16 O O4' 128 . . . G 5 16.153 -12.521 -37.121 1 143.74 ? O4' 128 406 A 1 HETATM 17 C C3' 128 . . . G 5 15.576 -13.975 -38.909 1 172.07 ? C3' 128 406 A 1 HETATM 18 O O3' 128 . . . G 5 14.195 -14.117 -39.233 1 179.07 ? O3' 128 406 A 1 HETATM 19 C C2' 128 . . . G 5 15.923 -12.583 -39.447 1 156.41 ? C2' 128 406 A 1 HETATM 20 O O2' 128 . . . G 5 14.866 -12.309 -40.365 1 143.82 ? O2' 128 406 A 1 HETATM 21 C C1' 128 . . . G 5 15.767 -11.706 -38.209 1 139.74 ? C1' 128 406 A 1 HETATM 22 N N9 128 . . . G 5 16.616 -10.52 -38.223 1 129.85 ? N9 128 406 A 1 HETATM 23 C C8 128 . . . G 5 16.218 -9.223 -38.404 1 130.03 ? C8 128 406 A 1 HETATM 24 N N7 128 . . . G 5 17.197 -8.349 -38.366 1 117.69 ? N7 128 406 A 1 HETATM 25 C C5 128 . . . G 5 18.321 -9.13 -38.144 1 119.05 ? C5 128 406 A 1 HETATM 26 C C6 128 . . . G 5 19.684 -8.808 -38 1 113.11 ? C6 128 406 A 1 HETATM 27 N N6 128 . . . G 5 20.159 -7.56 -38.032 1 100.59 ? N6 128 406 A 1 HETATM 28 N N1 128 . . . G 5 20.549 -9.826 -37.796 1 128.91 ? N1 128 406 A 1 HETATM 29 C C2 128 . . . G 5 20.072 -11.073 -37.733 1 137.14 ? C2 128 406 A 1 HETATM 30 N N3 128 . . . G 5 18.811 -11.498 -37.847 1 136.93 ? N3 128 406 A 1 HETATM 31 C C4 128 . . . G 5 17.979 -10.47 -38.054 1 135.14 ? C4 128 406 A 1 HETATM 32 C C1F 128 . . . G 5 13.936 -13.387 -40.427 1 156.06 ? C1F 128 406 A 1 HETATM 33 C C2F 128 . . . G 5 12.508 -12.92 -40.348 1 152.69 ? C2F 128 406 A 1 HETATM 34 C C3F 128 . . . G 5 11.552 -13.211 -41.305 1 164.14 ? C3F 128 406 A 1 HETATM 35 C C4F 128 . . . G 5 11.859 -13.968 -42.415 1 154.34 ? C4F 128 406 A 1 HETATM 36 C C5F 128 . . . G 5 13.156 -14.463 -42.608 1 153.33 ? C5F 128 406 A 1 HETATM 37 C C6F 128 . . . G 5 14.132 -14.198 -41.692 1 151.98 ? C6F 128 406 A 1 HETATM 38 N N2F 128 . . . G 5 12.14 -12.149 -39.223 1 152.65 ? N2F 128 406 A 1 HETATM 39 N N4F 128 . . . G 5 10.843 -14.236 -43.323 1 153.1 ? N4F 128 406 A 1 HETATM 40 N N6F 128 . . . G 5 15.425 -14.762 -41.972 1 148.43 ? N6F 128 406 A 1 HETATM 41 O O2F 128 . . . G 5 12.99 -11.898 -38.357 1 141.96 ? O2F 128 406 A 1 HETATM 42 O O3F 128 . . . G 5 10.974 -11.74 -39.129 1 163.39 ? O3F 128 406 A 1 HETATM 43 O O4F 128 . . . G 5 9.677 -13.85 -43.291 1 142.59 ? O4F 128 406 A 1 HETATM 44 O O5F 128 . . . G 5 11.166 -14.999 -44.371 1 148.49 ? O5F 128 406 A 1 HETATM 45 O O6F 128 . . . G 5 16.397 -14.012 -41.964 1 152.91 ? O6F 128 406 A 1 HETATM 46 O O7F 128 . . . G 5 15.492 -15.966 -42.204 1 153.03 ? O7F 128 406 A 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 46 #