data_5XW6 # _model_server_result.job_id l2bQdD2eK7s0awAjNa9mwQ _model_server_result.datetime_utc '2024-10-20 00:43:55' _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 5xw6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":502}' # _entry.id 5XW6 # _exptl.entry_id 5XW6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 718.27 _entity.id 3 _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 3 _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 5XW6 _cell.length_a 113.038 _cell.length_b 113.038 _cell.length_c 333.472 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XW6 _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 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,I _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 ? 3 E N N ? 3 F N N ? 3 H 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 disulf ? disulf1 A SG CYS 86 C CYS 107 1_555 A SG CYS 135 C CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf2 A SG CYS 96 C CYS 117 1_555 A SG CYS 119 C CYS 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? disulf ? disulf3 A SG CYS 102 C CYS 123 1_555 A SG CYS 129 C CYS 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? disulf ? disulf4 A SG CYS 183 C CYS 204 1_555 A SG CYS 193 C CYS 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 A SG CYS 227 C CYS 248 1_555 A SG CYS 236 C CYS 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf6 B SG CYS 86 A CYS 107 1_555 B SG CYS 135 A CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? disulf ? disulf7 B SG CYS 96 A CYS 117 1_555 B SG CYS 119 A CYS 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf8 B SG CYS 102 A CYS 123 1_555 B SG CYS 129 A CYS 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf9 B SG CYS 183 A CYS 204 1_555 B SG CYS 193 A CYS 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? disulf ? disulf10 B SG CYS 227 A CYS 248 1_555 B SG CYS 236 A CYS 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? disulf ? disulf11 C SG CYS 86 B CYS 107 1_555 C SG CYS 135 B CYS 156 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? disulf ? disulf12 C SG CYS 96 B CYS 117 1_555 C SG CYS 119 B CYS 140 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf13 C SG CYS 102 B CYS 123 1_555 C SG CYS 129 B CYS 150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? disulf ? disulf14 C SG CYS 183 B CYS 204 1_555 C SG CYS 193 B CYS 214 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf15 C SG CYS 227 B CYS 248 1_555 C SG CYS 236 B CYS 257 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? covale ? covale1 A ND2 ASN 123 C ASN 144 1_555 D C1 NAG . C NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale2 B ND2 ASN 123 A ASN 144 1_555 G C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale3 C ND2 ASN 123 B ASN 144 1_555 I C1 NAG . B NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 ? # _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 5XW6 _atom_sites.fract_transf_matrix[1][1] 0.008847 _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] 0.008847 _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] 0.002999 _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 D 2 NAG C 1 501 501 NAG NAG . E 3 128 C 1 502 401 128 128 . F 3 128 A 1 401 401 128 128 . G 2 NAG A 1 402 501 NAG NAG . H 3 128 B 1 401 401 128 128 . I 2 NAG B 1 402 501 NAG NAG . # 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 . . . E 3 -18.69 -22.563 -38.996 1 140.73 ? PG 128 502 C 1 HETATM 2 O O1G 128 . . . E 3 -19.324 -23.917 -38.806 1 104.22 -1 O1G 128 502 C 1 HETATM 3 O O2G 128 . . . E 3 -19.436 -21.725 -40.009 1 122.18 ? O2G 128 502 C 1 HETATM 4 O O3G 128 . . . E 3 -17.212 -22.657 -39.307 1 121.64 -1 O3G 128 502 C 1 HETATM 5 P PB 128 . . . E 3 -18.285 -22.023 -36.068 1 175.26 ? PB 128 502 C 1 HETATM 6 O O1B 128 . . . E 3 -17.123 -22.941 -36.057 1 143.95 -1 O1B 128 502 C 1 HETATM 7 O O2B 128 . . . E 3 -18.174 -20.716 -35.378 1 143.14 ? O2B 128 502 C 1 HETATM 8 O O3B 128 . . . E 3 -18.736 -21.756 -37.587 1 138 ? O3B 128 502 C 1 HETATM 9 P PA 128 . . . E 3 -20.412 -24.047 -35.861 1 124.55 ? PA 128 502 C 1 HETATM 10 O O1A 128 . . . E 3 -19.643 -25.279 -35.527 1 102.13 -1 O1A 128 502 C 1 HETATM 11 O O2A 128 . . . E 3 -20.926 -23.841 -37.243 1 123.59 ? O2A 128 502 C 1 HETATM 12 O O3A 128 . . . E 3 -19.573 -22.755 -35.456 1 127.98 ? O3A 128 502 C 1 HETATM 13 O O5' 128 . . . E 3 -21.643 -23.903 -34.859 1 112.18 ? O5' 128 502 C 1 HETATM 14 C C5' 128 . . . E 3 -22.828 -24.687 -35.136 1 98.07 ? C5' 128 502 C 1 HETATM 15 C C4' 128 . . . E 3 -23.836 -23.947 -34.304 1 97.26 ? C4' 128 502 C 1 HETATM 16 O O4' 128 . . . E 3 -23.385 -23.974 -32.939 1 104.75 ? O4' 128 502 C 1 HETATM 17 C C3' 128 . . . E 3 -23.835 -22.459 -34.611 1 105.9 ? C3' 128 502 C 1 HETATM 18 O O3' 128 . . . E 3 -24.803 -22.078 -35.606 1 116.14 ? O3' 128 502 C 1 HETATM 19 C C2' 128 . . . E 3 -24.338 -21.827 -33.308 1 102.1 ? C2' 128 502 C 1 HETATM 20 O O2' 128 . . . E 3 -25.731 -21.731 -33.551 1 118.37 ? O2' 128 502 C 1 HETATM 21 C C1' 128 . . . E 3 -23.986 -22.89 -32.246 1 94.23 ? C1' 128 502 C 1 HETATM 22 N N9 128 . . . E 3 -23.02 -22.432 -31.266 1 79.02 ? N9 128 502 C 1 HETATM 23 C C8 128 . . . E 3 -21.666 -22.297 -31.449 1 72.86 ? C8 128 502 C 1 HETATM 24 N N7 128 . . . E 3 -21.059 -21.851 -30.377 1 74.35 ? N7 128 502 C 1 HETATM 25 C C5 128 . . . E 3 -22.066 -21.697 -29.434 1 70.54 ? C5 128 502 C 1 HETATM 26 C C6 128 . . . E 3 -22.055 -21.256 -28.096 1 72.78 ? C6 128 502 C 1 HETATM 27 N N6 128 . . . E 3 -20.95 -20.87 -27.458 1 74.2 ? N6 128 502 C 1 HETATM 28 N N1 128 . . . E 3 -23.243 -21.219 -27.442 1 61.28 ? N1 128 502 C 1 HETATM 29 C C2 128 . . . E 3 -24.344 -21.605 -28.098 1 67.61 ? C2 128 502 C 1 HETATM 30 N N3 128 . . . E 3 -24.472 -22.031 -29.352 1 72.87 ? N3 128 502 C 1 HETATM 31 C C4 128 . . . E 3 -23.283 -22.053 -29.974 1 70.05 ? C4 128 502 C 1 HETATM 32 C C1F 128 . . . E 3 -25.868 -21.364 -34.936 1 112.72 ? C1F 128 502 C 1 HETATM 33 C C2F 128 . . . E 3 -27.267 -21.91 -35.15 1 112.29 ? C2F 128 502 C 1 HETATM 34 C C3F 128 . . . E 3 -28.347 -21.154 -35.511 1 121.61 ? C3F 128 502 C 1 HETATM 35 C C4F 128 . . . E 3 -28.236 -19.794 -35.713 1 118.76 ? C4F 128 502 C 1 HETATM 36 C C5F 128 . . . E 3 -27.008 -19.17 -35.592 1 108.72 ? C5F 128 502 C 1 HETATM 37 C C6F 128 . . . E 3 -25.859 -19.864 -35.241 1 113.8 ? C6F 128 502 C 1 HETATM 38 N N2F 128 . . . E 3 -27.511 -23.266 -34.937 1 126.17 ? N2F 128 502 C 1 HETATM 39 N N4F 128 . . . E 3 -29.389 -19.096 -36.056 1 123.97 ? N4F 128 502 C 1 HETATM 40 N N6F 128 . . . E 3 -24.678 -19.081 -35.161 1 127.59 ? N6F 128 502 C 1 HETATM 41 O O2F 128 . . . E 3 -26.573 -24.03 -34.616 1 137.73 -1 O2F 128 502 C 1 HETATM 42 O O3F 128 . . . E 3 -28.676 -23.7 -35.076 1 132.71 ? O3F 128 502 C 1 HETATM 43 O O4F 128 . . . E 3 -29.343 -17.748 -36.291 1 115.58 ? O4F 128 502 C 1 HETATM 44 O O5F 128 . . . E 3 -30.501 -19.682 -36.163 1 133.45 -1 O5F 128 502 C 1 HETATM 45 O O6F 128 . . . E 3 -24.761 -17.855 -35.406 1 131.97 -1 O6F 128 502 C 1 HETATM 46 O O7F 128 . . . E 3 -23.57 -19.584 -34.868 1 126.15 ? O7F 128 502 C 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 46 #