data_6YSO # _model_server_result.job_id dSdF1rU5c5DAgA3UwIkHmQ _model_server_result.datetime_utc '2024-11-24 18:00:55' _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 6yso # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1000}' # _entry.id 6YSO # _exptl.entry_id 6YSO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 718.27 _entity.id 2 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description "SPIRO(2,4,6-TRINITROBENZENE[1,2A]-2O',3O'-METHYLENE-ADENINE-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 107.05 _cell.angle_gamma 90 _cell.entry_id 6YSO _cell.length_a 131.14 _cell.length_b 94.39 _cell.length_c 135.11 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YSO _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,I,Q 1 1 B,J,K,L,M,N,O,P,R 2 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 ? 2 C N N ? 2 J 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 metalc ? metalc1 A OE1 GLN 244 A GLN 244 1_555 I K K . A K 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.797 ? metalc ? metalc2 A OD1 ASP 351 A ASP 351 1_555 E V VN4 . A VN4 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc3 A OD2 ASP 351 A ASP 351 1_555 F MG MG . A MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? metalc ? metalc4 A O THR 353 A THR 353 1_555 F MG MG . A MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? metalc ? metalc5 A OD1 ASN 628 A ASN 628 1_555 G MG MG . A MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.927 ? metalc ? metalc6 A OD1 ASP 703 A ASP 703 1_555 F MG MG . A MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc7 A O LEU 711 A LEU 711 1_555 I K K . A K 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? metalc ? metalc8 A O LYS 712 A LYS 712 1_555 I K K . A K 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.218 ? metalc ? metalc9 A O ALA 714 A ALA 714 1_555 I K K . A K 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.838 ? metalc ? metalc10 A OE1 GLU 732 A GLU 732 1_555 I K K . A K 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.832 ? metalc ? metalc11 A OE2 GLU 732 A GLU 732 1_555 I K K . A K 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.813 ? metalc ? metalc12 C O3G 128 . A 128 1000 1_555 G MG MG . A MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc13 C O1B 128 . A 128 1000 1_555 G MG MG . A MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.854 ? metalc ? metalc14 E O3 VN4 . A VN4 1002 1_555 F MG MG . A MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? metalc ? metalc15 E V VN4 . A VN4 1002 1_555 Q O HOH . A HOH 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc16 F MG MG . A MG 1003 1_555 Q O HOH . A HOH 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc17 F MG MG . A MG 1003 1_555 Q O HOH . A HOH 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.897 ? metalc ? metalc18 G MG MG . A MG 1004 1_555 Q O HOH . A HOH 1103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc19 B OE1 GLN 244 B GLN 244 1_555 P K K . B K 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.753 ? metalc ? metalc20 B OD1 ASP 351 B ASP 351 1_555 L V VN4 . B VN4 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc21 B OD2 ASP 351 B ASP 351 1_555 M MG MG . B MG 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? metalc ? metalc22 B O THR 353 B THR 353 1_555 M MG MG . B MG 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc23 B OD1 ASN 628 B ASN 628 1_555 N MG MG . B MG 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.91 ? metalc ? metalc24 B OD1 ASP 703 B ASP 703 1_555 M MG MG . B MG 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc25 B O LEU 711 B LEU 711 1_555 P K K . B K 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.722 ? metalc ? metalc26 B O LYS 712 B LYS 712 1_555 P K K . B K 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.29 ? metalc ? metalc27 B O ALA 714 B ALA 714 1_555 P K K . B K 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.893 ? metalc ? metalc28 B OE1 GLU 732 B GLU 732 1_555 P K K . B K 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.814 ? metalc ? metalc29 B OE2 GLU 732 B GLU 732 1_555 P K K . B K 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.778 ? metalc ? metalc30 J O3G 128 . B 128 2000 1_555 N MG MG . B MG 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.219 ? metalc ? metalc31 J O2B 128 . B 128 2000 1_555 N MG MG . B MG 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.641 ? metalc ? metalc32 L O3 VN4 . B VN4 2002 1_555 M MG MG . B MG 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.377 ? metalc ? metalc33 L V VN4 . B VN4 2002 1_555 R O HOH . B HOH 2101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? metalc ? metalc34 M MG MG . B MG 2003 1_555 R O HOH . B HOH 2102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc35 M MG MG . B MG 2003 1_555 R O HOH . B HOH 2104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc36 N MG MG . B MG 2004 1_555 R O HOH . B HOH 2103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? # _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 6YSO _atom_sites.fract_transf_matrix[1][1] 0.007625 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002339 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010594 _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] 0.007742 _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 C 2 128 A 1 1000 1000 128 128 . D 3 TG1 A 1 1001 1001 TG1 TG1 . E 4 VN4 A 1 1002 1002 VN4 VN4 . F 5 MG A 1 1003 1003 MG MG . G 5 MG A 1 1004 1004 MG MG . H 6 CL A 1 1005 1005 CL CL . I 7 K A 1 1006 1006 K K . J 2 128 B 1 2000 2000 128 128 . K 3 TG1 B 1 2001 2001 TG1 TG1 . L 4 VN4 B 1 2002 2002 VN4 VN4 . M 5 MG B 1 2003 2003 MG MG . N 5 MG B 1 2004 2004 MG MG . O 6 CL B 1 2005 2005 CL CL . P 7 K B 1 2006 2006 K K . Q 8 HOH A 1 1101 4 HOH HOH . Q 8 HOH A 2 1102 3 HOH HOH . Q 8 HOH A 3 1103 1 HOH HOH . Q 8 HOH A 4 1104 5 HOH HOH . R 8 HOH B 1 2101 7 HOH HOH . R 8 HOH B 2 2102 8 HOH HOH . R 8 HOH B 3 2103 6 HOH HOH . R 8 HOH B 4 2104 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 . . . C 2 124.628 21.941 21.76 1 244.14 ? PG 128 1000 A 1 HETATM 2 O O1G 128 . . . C 2 123.108 21.763 22.222 1 269.7 ? O1G 128 1000 A 1 HETATM 3 O O2G 128 . . . C 2 125.15 23.291 22.436 1 249.31 ? O2G 128 1000 A 1 HETATM 4 O O3G 128 . . . C 2 124.6 22.104 20.315 1 292.55 ? O3G 128 1000 A 1 HETATM 5 P PB 128 . . . C 2 125.656 19.065 21.606 1 145.17 ? PB 128 1000 A 1 HETATM 6 O O1B 128 . . . C 2 124.81 19.122 20.469 1 144.22 ? O1B 128 1000 A 1 HETATM 7 O O2B 128 . . . C 2 126.95 18.785 21.182 1 138.79 ? O2B 128 1000 A 1 HETATM 8 O O3B 128 . . . C 2 125.721 20.697 22.383 1 194.78 ? O3B 128 1000 A 1 HETATM 9 P PA 128 . . . C 2 123.551 17.191 23.116 1 131.37 ? PA 128 1000 A 1 HETATM 10 O O1A 128 . . . C 2 122.249 17.726 22.389 1 139.92 ? O1A 128 1000 A 1 HETATM 11 O O2A 128 . . . C 2 123.642 17.533 24.589 1 155.49 ? O2A 128 1000 A 1 HETATM 12 O O3A 128 . . . C 2 124.941 17.807 22.529 1 123.64 ? O3A 128 1000 A 1 HETATM 13 O O5' 128 . . . C 2 123.748 15.59 22.697 1 120.78 ? O5' 128 1000 A 1 HETATM 14 C C5' 128 . . . C 2 123.192 15.043 21.47 1 117.44 ? C5' 128 1000 A 1 HETATM 15 C C4' 128 . . . C 2 124.158 13.89 20.869 1 110.79 ? C4' 128 1000 A 1 HETATM 16 O O4' 128 . . . C 2 123.886 13.92 19.412 1 108.95 ? O4' 128 1000 A 1 HETATM 17 C C3' 128 . . . C 2 125.6 14.031 20.829 1 111.55 ? C3' 128 1000 A 1 HETATM 18 O O3' 128 . . . C 2 126.2 12.851 21.433 1 126.78 ? O3' 128 1000 A 1 HETATM 19 C C2' 128 . . . C 2 126.105 14.136 19.322 1 110.74 ? C2' 128 1000 A 1 HETATM 20 O O2' 128 . . . C 2 127.01 13.043 18.99 1 116.98 ? O2' 128 1000 A 1 HETATM 21 C C1' 128 . . . C 2 124.846 14.051 18.406 1 116.24 ? C1' 128 1000 A 1 HETATM 22 N N9 128 . . . C 2 124.503 15.287 17.619 1 95.61 ? N9 128 1000 A 1 HETATM 23 C C8 128 . . . C 2 123.799 16.407 17.936 1 104.74 ? C8 128 1000 A 1 HETATM 24 N N7 128 . . . C 2 123.698 17.292 16.992 1 114.75 ? N7 128 1000 A 1 HETATM 25 C C5 128 . . . C 2 124.368 16.754 15.968 1 106.16 ? C5 128 1000 A 1 HETATM 26 C C6 128 . . . C 2 124.586 17.298 14.651 1 96.15 ? C6 128 1000 A 1 HETATM 27 N N6 128 . . . C 2 124.075 18.507 14.339 1 99.51 ? N6 128 1000 A 1 HETATM 28 N N1 128 . . . C 2 125.341 16.554 13.687 1 102.5 ? N1 128 1000 A 1 HETATM 29 C C2 128 . . . C 2 125.835 15.326 14.068 1 106.59 ? C2 128 1000 A 1 HETATM 30 N N3 128 . . . C 2 125.611 14.829 15.334 1 90.04 ? N3 128 1000 A 1 HETATM 31 C C4 128 . . . C 2 124.883 15.506 16.323 1 94.8 ? C4 128 1000 A 1 HETATM 32 C C1F 128 . . . C 2 127.054 12.255 20.315 1 122.3 ? C1F 128 1000 A 1 HETATM 33 C C2F 128 . . . C 2 128.574 12.223 20.676 1 116.16 ? C2F 128 1000 A 1 HETATM 34 C C3F 128 . . . C 2 129.257 10.998 20.862 1 119.28 ? C3F 128 1000 A 1 HETATM 35 C C4F 128 . . . C 2 128.737 9.708 20.764 1 135.01 ? C4F 128 1000 A 1 HETATM 36 C C5F 128 . . . C 2 127.354 9.627 20.437 1 128.04 ? C5F 128 1000 A 1 HETATM 37 C C6F 128 . . . C 2 126.443 10.811 20.198 1 128.16 ? C6F 128 1000 A 1 HETATM 38 N N2F 128 . . . C 2 129.376 13.425 20.843 1 137.74 ? N2F 128 1000 A 1 HETATM 39 N N4F 128 . . . C 2 129.421 8.566 20.948 1 144.96 ? N4F 128 1000 A 1 HETATM 40 N N6F 128 . . . C 2 125.063 10.405 19.878 1 141.53 ? N6F 128 1000 A 1 HETATM 41 O O2F 128 . . . C 2 128.953 14.536 20.721 1 141.85 ? O2F 128 1000 A 1 HETATM 42 O O3F 128 . . . C 2 130.566 13.378 21.127 1 150.85 ? O3F 128 1000 A 1 HETATM 43 O O4F 128 . . . C 2 128.928 7.447 20.853 1 124.51 ? O4F 128 1000 A 1 HETATM 44 O O5F 128 . . . C 2 130.601 8.567 21.228 1 156.01 ? O5F 128 1000 A 1 HETATM 45 O O6F 128 . . . C 2 124.186 11.266 19.654 1 149.89 ? O6F 128 1000 A 1 HETATM 46 O O7F 128 . . . C 2 124.654 9.3 19.803 1 151.01 ? O7F 128 1000 A 1 # _model_server_stats.io_time_ms 41 _model_server_stats.parse_time_ms 32 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 371 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 46 #