data_5NCQ # _model_server_result.job_id PXL9ve1lks-fRoTpOOoCpA _model_server_result.datetime_utc '2024-11-23 11:24:07' _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 5ncq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1001}' # _entry.id 5NCQ # _exptl.entry_id 5NCQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 718.27 _entity.id 2 _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 90 _cell.entry_id 5NCQ _cell.length_a 125.62 _cell.length_b 224.63 _cell.length_c 57.05 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5NCQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 2 _struct_asym.id B _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 metalc ? metalc1 A O LYS 712 A LYS 712 1_555 C K K . A K 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.861 ? metalc ? metalc2 A O ALA 714 A ALA 714 1_555 C K K . A K 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.901 ? metalc ? metalc3 A OE1 GLU 732 A GLU 732 1_555 C K K . A K 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.055 ? metalc ? metalc4 A OE2 GLU 732 A GLU 732 1_555 C K K . A K 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.389 ? metalc ? metalc5 C K K . A K 1002 1_555 G O HOH . A HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.816 ? metalc ? metalc6 C K K . A K 1002 1_555 G O HOH . A HOH 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.066 ? # _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 5NCQ _atom_sites.fract_transf_matrix[1][1] 0.007961 _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] 0.004452 _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] 0.017528 _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 2 128 A 1 1001 1001 128 128 . C 3 K A 1 1002 1002 K K . D 4 PCW A 1 1003 1005 PCW PCW . E 4 PCW A 1 1004 1006 PCW PCW . F 5 8T8 A 1 1005 1007 8T8 8T8 . G 6 HOH A 1 1101 1004 HOH HOH . G 6 HOH A 2 1102 1003 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 . . . B 2 13.863 61.62 0.009 1 114.99 ? PG 128 1001 A 1 HETATM 2 O O1G 128 . . . B 2 13.85 60.791 1.268 1 110.38 ? O1G 128 1001 A 1 HETATM 3 O O2G 128 . . . B 2 13.746 60.734 -1.207 1 108.25 ? O2G 128 1001 A 1 HETATM 4 O O3G 128 . . . B 2 15.099 62.483 -0.038 1 118.93 ? O3G 128 1001 A 1 HETATM 5 P PB 128 . . . B 2 12.356 64.014 -0.437 1 126.8 ? PB 128 1001 A 1 HETATM 6 O O1B 128 . . . B 2 13.671 64.459 -1.025 1 126.3 ? O1B 128 1001 A 1 HETATM 7 O O2B 128 . . . B 2 11.711 64.838 0.652 1 112.72 ? O2B 128 1001 A 1 HETATM 8 O O3B 128 . . . B 2 12.52 62.515 0.146 1 143.97 ? O3B 128 1001 A 1 HETATM 9 P PA 128 . . . B 2 11.222 64.919 -2.83 1 91.01 ? PA 128 1001 A 1 HETATM 10 O O1A 128 . . . B 2 12.579 65.034 -3.5 1 88.49 ? O1A 128 1001 A 1 HETATM 11 O O2A 128 . . . B 2 10.001 64.636 -3.684 1 105.69 ? O2A 128 1001 A 1 HETATM 12 O O3A 128 . . . B 2 11.284 63.848 -1.626 1 104.44 ? O3A 128 1001 A 1 HETATM 13 O O5' 128 . . . B 2 10.937 66.302 -2.051 1 88.38 ? O5' 128 1001 A 1 HETATM 14 C C5' 128 . . . B 2 11.576 67.468 -2.56 1 98.04 ? C5' 128 1001 A 1 HETATM 15 C C4' 128 . . . B 2 10.954 68.762 -2.048 1 82.46 ? C4' 128 1001 A 1 HETATM 16 O O4' 128 . . . B 2 9.712 68.583 -1.348 1 74.51 ? O4' 128 1001 A 1 HETATM 17 C C3' 128 . . . B 2 11.904 69.504 -1.122 1 94.63 ? C3' 128 1001 A 1 HETATM 18 O O3' 128 . . . B 2 12.447 70.676 -1.729 1 107.19 ? O3' 128 1001 A 1 HETATM 19 C C2' 128 . . . B 2 11.042 70.007 0.021 1 95.21 ? C2' 128 1001 A 1 HETATM 20 O O2' 128 . . . B 2 11.094 71.434 -0.063 1 101.39 ? O2' 128 1001 A 1 HETATM 21 C C1' 128 . . . B 2 9.645 69.459 -0.213 1 83.18 ? C1' 128 1001 A 1 HETATM 22 N N9 128 . . . B 2 9.127 68.797 1.011 1 79.45 ? N9 128 1001 A 1 HETATM 23 C C8 128 . . . B 2 9.627 67.712 1.618 1 83.37 ? C8 128 1001 A 1 HETATM 24 N N7 128 . . . B 2 8.981 67.354 2.703 1 87.72 ? N7 128 1001 A 1 HETATM 25 C C5 128 . . . B 2 7.986 68.314 2.812 1 87.82 ? C5 128 1001 A 1 HETATM 26 C C6 128 . . . B 2 6.969 68.519 3.73 1 96.75 ? C6 128 1001 A 1 HETATM 27 N N6 128 . . . B 2 6.814 67.68 4.782 1 94.08 ? N6 128 1001 A 1 HETATM 28 N N1 128 . . . B 2 6.147 69.574 3.548 1 96.26 ? N1 128 1001 A 1 HETATM 29 C C2 128 . . . B 2 6.347 70.37 2.491 1 92.33 ? C2 128 1001 A 1 HETATM 30 N N3 128 . . . B 2 7.287 70.275 1.542 1 86.46 ? N3 128 1001 A 1 HETATM 31 C C4 128 . . . B 2 8.095 69.207 1.76 1 83.57 ? C4 128 1001 A 1 HETATM 32 C C1F 128 . . . B 2 12.086 71.842 -0.998 1 103.61 ? C1F 128 1001 A 1 HETATM 33 C C2F 128 . . . B 2 13.312 72.365 -0.264 1 105.77 ? C2F 128 1001 A 1 HETATM 34 C C3F 128 . . . B 2 13.82 73.636 -0.548 1 113.48 ? C3F 128 1001 A 1 HETATM 35 C C4F 128 . . . B 2 13.224 74.491 -1.474 1 122.05 ? C4F 128 1001 A 1 HETATM 36 C C5F 128 . . . B 2 12.101 74.095 -2.175 1 111.33 ? C5F 128 1001 A 1 HETATM 37 C C6F 128 . . . B 2 11.518 72.853 -1.977 1 103.33 ? C6F 128 1001 A 1 HETATM 38 N N2F 128 . . . B 2 14.121 71.573 0.789 1 108.16 ? N2F 128 1001 A 1 HETATM 39 N N4F 128 . . . B 2 13.755 75.706 -1.688 1 136.86 ? N4F 128 1001 A 1 HETATM 40 N N6F 128 . . . B 2 10.379 72.596 -2.763 1 107.31 ? N6F 128 1001 A 1 HETATM 41 O O2F 128 . . . B 2 13.808 70.449 1.139 1 117.5 ? O2F 128 1001 A 1 HETATM 42 O O3F 128 . . . B 2 15.088 72.128 1.29 1 105.56 ? O3F 128 1001 A 1 HETATM 43 O O4F 128 . . . B 2 13.258 76.473 -2.495 1 137.58 ? O4F 128 1001 A 1 HETATM 44 O O5F 128 . . . B 2 14.746 76.043 -1.067 1 146.33 ? O5F 128 1001 A 1 HETATM 45 O O6F 128 . . . B 2 9.993 73.46 -3.538 1 97.85 ? O6F 128 1001 A 1 HETATM 46 O O7F 128 . . . B 2 9.808 71.527 -2.664 1 120.93 ? O7F 128 1001 A 1 # _model_server_stats.io_time_ms 81 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 46 #