data_6YAA # _model_server_result.job_id 6igbEuAQ1O--Bu5CFVu9_A _model_server_result.datetime_utc '2024-10-19 19:27:39' _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 6yaa # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1001}' # _entry.id 6YAA # _exptl.entry_id 6YAA _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 6YAA _cell.length_a 71.632 _cell.length_b 71.632 _cell.length_c 588.306 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YAA _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall 'P 4abw 2nw' _symmetry.space_group_name_H-M 'P 41 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 _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 disulf ? disulf1 A SG CYS 876 A CYS 876 1_555 A SG CYS 888 A CYS 888 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc1 A O LEU 711 A LEU 711 1_555 D K K . A K 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? metalc ? metalc2 A O LYS 712 A LYS 712 1_555 D K K . A K 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.431 ? metalc ? metalc3 A O ALA 714 A ALA 714 1_555 D K K . A K 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.938 ? metalc ? metalc4 A OE1 GLU 732 A GLU 732 1_555 D K K . A K 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.142 ? metalc ? metalc5 A OE2 GLU 732 A GLU 732 1_555 D K K . A K 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.765 ? # _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 6YAA _atom_sites.fract_transf_matrix[1][1] 0.01396 _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] 0.01396 _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] 0.0017 _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 OHW A 1 1002 1101 OHW 520 . D 4 K A 1 1003 1201 K K . # 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 -0.361 32.861 -21.915 1 153.59 ? PG 128 1001 A 1 HETATM 2 O O1G 128 . . . B 2 -0.926 31.553 -22.64 1 153.59 ? O1G 128 1001 A 1 HETATM 3 O O2G 128 . . . B 2 -1.622 33.772 -21.558 1 153.59 ? O2G 128 1001 A 1 HETATM 4 O O3G 128 . . . B 2 0.514 33.546 -22.853 1 153.59 ? O3G 128 1001 A 1 HETATM 5 P PB 128 . . . B 2 -0.28 32.99 -18.782 1 153.59 ? PB 128 1001 A 1 HETATM 6 O O1B 128 . . . B 2 -0.905 31.868 -18.175 1 153.59 ? O1B 128 1001 A 1 HETATM 7 O O2B 128 . . . B 2 0.856 33.298 -18.052 1 153.59 ? O2B 128 1001 A 1 HETATM 8 O O3B 128 . . . B 2 0.402 32.469 -20.375 1 153.59 ? O3B 128 1001 A 1 HETATM 9 P PA 128 . . . B 2 -1.695 35.298 -17.332 1 153.59 ? PA 128 1001 A 1 HETATM 10 O O1A 128 . . . B 2 -0.393 36.117 -16.93 1 153.59 ? O1A 128 1001 A 1 HETATM 11 O O2A 128 . . . B 2 -2.884 36.165 -17.703 1 153.59 ? O2A 128 1001 A 1 HETATM 12 O O3A 128 . . . B 2 -1.41 34.258 -18.555 1 153.59 ? O3A 128 1001 A 1 HETATM 13 O O5' 128 . . . B 2 -1.973 34.14 -16.158 1 153.59 ? O5' 128 1001 A 1 HETATM 14 C C5' 128 . . . B 2 -0.9 33.457 -15.461 1 153.59 ? C5' 128 1001 A 1 HETATM 15 C C4' 128 . . . B 2 -0.778 34.007 -13.944 1 153.59 ? C4' 128 1001 A 1 HETATM 16 O O4' 128 . . . B 2 -2.204 34.105 -13.495 1 153.59 ? O4' 128 1001 A 1 HETATM 17 C C3' 128 . . . B 2 -0.314 33.08 -12.931 1 153.59 ? C3' 128 1001 A 1 HETATM 18 O O3' 128 . . . B 2 0.822 33.519 -12.134 1 153.59 ? O3' 128 1001 A 1 HETATM 19 C C2' 128 . . . B 2 -1.478 32.666 -11.94 1 153.59 ? C2' 128 1001 A 1 HETATM 20 O O2' 128 . . . B 2 -1.104 32.787 -10.542 1 153.59 ? O2' 128 1001 A 1 HETATM 21 C C1' 128 . . . B 2 -2.74 33.46 -12.367 1 153.59 ? C1' 128 1001 A 1 HETATM 22 N N9 128 . . . B 2 -4.051 32.698 -12.413 1 153.59 ? N9 128 1001 A 1 HETATM 23 C C8 128 . . . B 2 -4.893 32.102 -13.309 1 153.59 ? C8 128 1001 A 1 HETATM 24 N N7 128 . . . B 2 -5.948 31.524 -12.795 1 153.59 ? N7 128 1001 A 1 HETATM 25 C C5 128 . . . B 2 -5.824 31.727 -11.479 1 153.59 ? C5 128 1001 A 1 HETATM 26 C C6 128 . . . B 2 -6.671 31.331 -10.373 1 153.59 ? C6 128 1001 A 1 HETATM 27 N N6 128 . . . B 2 -7.8 30.631 -10.591 1 153.59 ? N6 128 1001 A 1 HETATM 28 N N1 128 . . . B 2 -6.319 31.66 -9.024 1 153.59 ? N1 128 1001 A 1 HETATM 29 C C2 128 . . . B 2 -5.164 32.366 -8.821 1 153.59 ? C2 128 1001 A 1 HETATM 30 N N3 128 . . . B 2 -4.379 32.731 -9.886 1 153.59 ? N3 128 1001 A 1 HETATM 31 C C4 128 . . . B 2 -4.658 32.44 -11.225 1 153.59 ? C4 128 1001 A 1 HETATM 32 C C1F 128 . . . B 2 0.355 33.256 -10.698 1 153.59 ? C1F 128 1001 A 1 HETATM 33 C C2F 128 . . . B 2 1.091 31.954 -10.247 1 153.59 ? C2F 128 1001 A 1 HETATM 34 C C3F 128 . . . B 2 2.002 31.98 -9.167 1 153.59 ? C3F 128 1001 A 1 HETATM 35 C C4F 128 . . . B 2 2.386 33.065 -8.375 1 153.59 ? C4F 128 1001 A 1 HETATM 36 C C5F 128 . . . B 2 1.764 34.312 -8.71 1 153.59 ? C5F 128 1001 A 1 HETATM 37 C C6F 128 . . . B 2 0.755 34.512 -9.833 1 153.59 ? C6F 128 1001 A 1 HETATM 38 N N2F 128 . . . B 2 0.909 30.64 -10.873 1 153.59 ? N2F 128 1001 A 1 HETATM 39 N N4F 128 . . . B 2 3.276 32.979 -7.356 1 153.59 ? N4F 128 1001 A 1 HETATM 40 N N6F 128 . . . B 2 0.27 35.902 -9.962 1 153.59 ? N6F 128 1001 A 1 HETATM 41 O O2F 128 . . . B 2 0.194 30.382 -11.798 1 153.59 ? O2F 128 1001 A 1 HETATM 42 O O3F 128 . . . B 2 1.517 29.66 -10.469 1 153.59 ? O3F 128 1001 A 1 HETATM 43 O O4F 128 . . . B 2 3.646 33.894 -6.63 1 153.59 ? O4F 128 1001 A 1 HETATM 44 O O5F 128 . . . B 2 3.805 31.926 -7.07 1 153.59 ? O5F 128 1001 A 1 HETATM 45 O O6F 128 . . . B 2 0.695 36.778 -9.184 1 153.59 ? O6F 128 1001 A 1 HETATM 46 O O7F 128 . . . B 2 -0.514 36.314 -10.751 1 153.59 ? O7F 128 1001 A 1 # _model_server_stats.io_time_ms 107 _model_server_stats.parse_time_ms 81 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 269 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 46 #