data_6YSO # _model_server_result.job_id s_dfEKE4Gs-Lqrsc5rTvCA _model_server_result.datetime_utc '2025-02-17 21:26:57' _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":"J","auth_seq_id":2000}' # _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 . . . J 2 118.443 58.298 39.449 1 145.74 ? PG 128 2000 B 1 HETATM 2 O O1G 128 . . . J 2 117.534 59.474 38.861 1 153.12 ? O1G 128 2000 B 1 HETATM 3 O O2G 128 . . . J 2 119.199 57.635 38.208 1 152.2 ? O2G 128 2000 B 1 HETATM 4 O O3G 128 . . . J 2 117.526 57.337 40.039 1 158.49 ? O3G 128 2000 B 1 HETATM 5 P PB 128 . . . J 2 119.365 60.37 41.414 1 122.8 ? PB 128 2000 B 1 HETATM 6 O O1B 128 . . . J 2 120.322 60.587 42.439 1 117.62 ? O1B 128 2000 B 1 HETATM 7 O O2B 128 . . . J 2 118.119 60.137 41.988 1 122.13 ? O2B 128 2000 B 1 HETATM 8 O O3B 128 . . . J 2 119.749 58.868 40.493 1 128.18 ? O3B 128 2000 B 1 HETATM 9 P PA 128 . . . J 2 118.751 63.244 40.184 1 165.07 ? PA 128 2000 B 1 HETATM 10 O O1A 128 . . . J 2 117.178 63.146 40.01 1 158.01 ? O1A 128 2000 B 1 HETATM 11 O O2A 128 . . . J 2 119.5 63.728 38.959 1 172.62 ? O2A 128 2000 B 1 HETATM 12 O O3A 128 . . . J 2 119.464 61.819 40.506 1 157.39 ? O3A 128 2000 B 1 HETATM 13 O O5' 128 . . . J 2 119.043 64.022 41.626 1 148.19 ? O5' 128 2000 B 1 HETATM 14 C C5' 128 . . . J 2 117.983 64.801 42.234 1 144.52 ? C5' 128 2000 B 1 HETATM 15 C C4' 128 . . . J 2 118.302 65.219 43.76 1 142.18 ? C4' 128 2000 B 1 HETATM 16 O O4' 128 . . . J 2 117.165 64.688 44.538 1 138.47 ? O4' 128 2000 B 1 HETATM 17 C C3' 128 . . . J 2 119.391 64.76 44.598 1 140.93 ? C3' 128 2000 B 1 HETATM 18 O O3' 128 . . . J 2 120.062 65.959 45.053 1 145.28 ? O3' 128 2000 B 1 HETATM 19 C C2' 128 . . . J 2 118.82 64.001 45.881 1 146.18 ? C2' 128 2000 B 1 HETATM 20 O O2' 128 . . . J 2 119.138 64.726 47.112 1 151.87 ? O2' 128 2000 B 1 HETATM 21 C C1' 128 . . . J 2 117.271 64.006 45.746 1 140.27 ? C1' 128 2000 B 1 HETATM 22 N N9 128 . . . J 2 116.541 62.698 45.651 1 140.21 ? N9 128 2000 B 1 HETATM 23 C C8 128 . . . J 2 116.475 61.703 44.726 1 143.25 ? C8 128 2000 B 1 HETATM 24 N N7 128 . . . J 2 115.697 60.709 45.04 1 147.77 ? N7 128 2000 B 1 HETATM 25 C C5 128 . . . J 2 115.207 61.041 46.24 1 138.91 ? C5 128 2000 B 1 HETATM 26 C C6 128 . . . J 2 114.288 60.321 47.084 1 139.72 ? C6 128 2000 B 1 HETATM 27 N N6 128 . . . J 2 113.804 59.131 46.678 1 143.17 ? N6 128 2000 B 1 HETATM 28 N N1 128 . . . J 2 113.896 60.873 48.347 1 138.19 ? N1 128 2000 B 1 HETATM 29 C C2 128 . . . J 2 114.421 62.092 48.71 1 133.85 ? C2 128 2000 B 1 HETATM 30 N N3 128 . . . J 2 115.294 62.758 47.886 1 134.68 ? N3 128 2000 B 1 HETATM 31 C C4 128 . . . J 2 115.716 62.272 46.644 1 137.67 ? C4 128 2000 B 1 HETATM 32 C C1F 128 . . . J 2 119.901 65.949 46.569 1 150.35 ? C1F 128 2000 B 1 HETATM 33 C C2F 128 . . . J 2 121.324 65.918 47.204 1 144.42 ? C2F 128 2000 B 1 HETATM 34 C C3F 128 . . . J 2 121.896 67.087 47.757 1 144.74 ? C3F 128 2000 B 1 HETATM 35 C C4F 128 . . . J 2 121.312 68.349 47.859 1 161.98 ? C4F 128 2000 B 1 HETATM 36 C C5F 128 . . . J 2 119.996 68.468 47.336 1 164.63 ? C5F 128 2000 B 1 HETATM 37 C C6F 128 . . . J 2 119.201 67.353 46.703 1 167.73 ? C6F 128 2000 B 1 HETATM 38 N N2F 128 . . . J 2 122.159 64.729 47.215 1 154.82 ? N2F 128 2000 B 1 HETATM 39 N N4F 128 . . . J 2 121.865 69.447 48.398 1 189.43 ? N4F 128 2000 B 1 HETATM 40 N N6F 128 . . . J 2 117.875 67.829 46.261 1 186.78 ? N6F 128 2000 B 1 HETATM 41 O O2F 128 . . . J 2 121.823 63.669 46.78 1 152.31 ? O2F 128 2000 B 1 HETATM 42 O O3F 128 . . . J 2 123.285 64.734 47.693 1 165.88 ? O3F 128 2000 B 1 HETATM 43 O O4F 128 . . . J 2 121.297 70.533 48.458 1 204.69 ? O4F 128 2000 B 1 HETATM 44 O O5F 128 . . . J 2 122.983 69.437 48.868 1 192.81 ? O5F 128 2000 B 1 HETATM 45 O O6F 128 . . . J 2 117.057 67.07 45.707 1 189.59 ? O6F 128 2000 B 1 HETATM 46 O O7F 128 . . . J 2 117.453 68.924 46.386 1 194.49 ? O7F 128 2000 B 1 # _model_server_stats.io_time_ms 47 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 46 #