data_5XW6 # _model_server_result.job_id pIEnH_PCtvF0mmkoOiWy9w _model_server_result.datetime_utc '2024-10-20 00:38:38' _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":"F","auth_seq_id":401}' # _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 . . . F 3 -1.521 -9.68 -9.516 1 140.66 ? PG 128 401 A 1 HETATM 2 O O1G 128 . . . F 3 -2.034 -11.093 -9.341 1 140.55 -1 O1G 128 401 A 1 HETATM 3 O O2G 128 . . . F 3 -1.867 -8.784 -8.344 1 127.85 ? O2G 128 401 A 1 HETATM 4 O O3G 128 . . . F 3 -1.921 -9.083 -10.846 1 137.63 -1 O3G 128 401 A 1 HETATM 5 P PB 128 . . . F 3 1.162 -10.596 -10.409 1 162.8 ? PB 128 401 A 1 HETATM 6 O O1B 128 . . . F 3 0.828 -10.527 -11.851 1 136.6 -1 O1B 128 401 A 1 HETATM 7 O O2B 128 . . . F 3 2.524 -10.223 -9.96 1 132.49 ? O2B 128 401 A 1 HETATM 8 O O3B 128 . . . F 3 0.096 -9.759 -9.553 1 133.89 ? O3B 128 401 A 1 HETATM 9 P PA 128 . . . F 3 0.748 -12.556 -8.352 1 150.71 ? PA 128 401 A 1 HETATM 10 O O1A 128 . . . F 3 0.788 -14.043 -8.302 1 124.81 -1 O1A 128 401 A 1 HETATM 11 O O2A 128 . . . F 3 -0.392 -11.862 -7.69 1 140.17 ? O2A 128 401 A 1 HETATM 12 O O3A 128 . . . F 3 0.851 -12.071 -9.872 1 129.95 ? O3A 128 401 A 1 HETATM 13 O O5' 128 . . . F 3 2.118 -11.957 -7.791 1 130.21 ? O5' 128 401 A 1 HETATM 14 C C5' 128 . . . F 3 2.306 -11.91 -6.364 1 114.63 ? C5' 128 401 A 1 HETATM 15 C C4' 128 . . . F 3 3.742 -11.511 -6.16 1 98.47 ? C4' 128 401 A 1 HETATM 16 O O4' 128 . . . F 3 4.613 -12.498 -6.736 1 101.6 ? O4' 128 401 A 1 HETATM 17 C C3' 128 . . . F 3 4.144 -10.277 -6.933 1 106.68 ? C3' 128 401 A 1 HETATM 18 O O3' 128 . . . F 3 3.867 -9.103 -6.16 1 121.74 ? O3' 128 401 A 1 HETATM 19 C C2' 128 . . . F 3 5.677 -10.386 -6.958 1 116.05 ? C2' 128 401 A 1 HETATM 20 O O2' 128 . . . F 3 6.052 -9.703 -5.768 1 130.32 ? O2' 128 401 A 1 HETATM 21 C C1' 128 . . . F 3 5.904 -11.909 -6.849 1 95.17 ? C1' 128 401 A 1 HETATM 22 N N9 128 . . . F 3 6.505 -12.51 -8.018 1 85.48 ? N9 128 401 A 1 HETATM 23 C C8 128 . . . F 3 5.848 -12.865 -9.169 1 80.12 ? C8 128 401 A 1 HETATM 24 N N7 128 . . . F 3 6.645 -13.412 -10.053 1 81.51 ? N7 128 401 A 1 HETATM 25 C C5 128 . . . F 3 7.89 -13.439 -9.44 1 75.45 ? C5 128 401 A 1 HETATM 26 C C6 128 . . . F 3 9.144 -13.912 -9.868 1 70.38 ? C6 128 401 A 1 HETATM 27 N N6 128 . . . F 3 9.339 -14.477 -11.06 1 62.23 ? N6 128 401 A 1 HETATM 28 N N1 128 . . . F 3 10.185 -13.789 -9.006 1 82.93 ? N1 128 401 A 1 HETATM 29 C C2 128 . . . F 3 9.967 -13.226 -7.809 1 64.05 ? C2 128 401 A 1 HETATM 30 N N3 128 . . . F 3 8.831 -12.752 -7.307 1 82.9 ? N3 128 401 A 1 HETATM 31 C C4 128 . . . F 3 7.818 -12.884 -8.181 1 83.45 ? C4 128 401 A 1 HETATM 32 C C1F 128 . . . F 3 5.127 -8.606 -5.626 1 131.27 ? C1F 128 401 A 1 HETATM 33 C C2F 128 . . . F 3 5.079 -8.41 -4.112 1 129.69 ? C2F 128 401 A 1 HETATM 34 C C3F 128 . . . F 3 5.294 -7.215 -3.475 1 118.54 ? C3F 128 401 A 1 HETATM 35 C C4F 128 . . . F 3 5.564 -6.067 -4.189 1 124.54 ? C4F 128 401 A 1 HETATM 36 C C5F 128 . . . F 3 5.637 -6.098 -5.568 1 122.86 ? C5F 128 401 A 1 HETATM 37 C C6F 128 . . . F 3 5.451 -7.259 -6.292 1 121.77 ? C6F 128 401 A 1 HETATM 38 N N2F 128 . . . F 3 4.815 -9.503 -3.276 1 135.52 ? N2F 128 401 A 1 HETATM 39 N N4F 128 . . . F 3 5.769 -4.872 -3.525 1 130.19 ? N4F 128 401 A 1 HETATM 40 N N6F 128 . . . F 3 5.559 -7.099 -7.699 1 124.68 ? N6F 128 401 A 1 HETATM 41 O O2F 128 . . . F 3 4.615 -10.638 -3.762 1 129.81 -1 O2F 128 401 A 1 HETATM 42 O O3F 128 . . . F 3 4.782 -9.318 -2.038 1 136.41 ? O3F 128 401 A 1 HETATM 43 O O4F 128 . . . F 3 5.693 -4.846 -2.153 1 136.18 ? O4F 128 401 A 1 HETATM 44 O O5F 128 . . . F 3 6.022 -3.812 -4.156 1 133.29 -1 O5F 128 401 A 1 HETATM 45 O O6F 128 . . . F 3 5.817 -5.956 -8.145 1 117.55 -1 O6F 128 401 A 1 HETATM 46 O O7F 128 . . . F 3 5.403 -8.057 -8.487 1 136.21 ? O7F 128 401 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 46 #