data_5A3S # _model_server_result.job_id MhkkJBpavn63swUmOE_m-Q _model_server_result.datetime_utc '2024-11-23 14:25:19' _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 5a3s # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":1002}' # _entry.id 5A3S # _exptl.entry_id 5A3S _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 718.27 _entity.id 4 _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 107.26 _cell.angle_gamma 90 _cell.entry_id 5A3S _cell.length_a 130.556 _cell.length_b 93.778 _cell.length_c 135.692 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5A3S _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 PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_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 ? 4 E N N ? 4 L 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 covale ? covale1 A C ACE 1 A ACE 0 1_555 A N MET 2 A MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 B C ACE 1 B ACE 0 1_555 B N MET 2 B MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 A OE1 GLN 245 A GLN 244 1_555 H K K . A K 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.85 ? metalc ? metalc2 A OD1 ASP 352 A ASP 351 1_555 D V VN4 . A VN4 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc3 A OD2 ASP 352 A ASP 351 1_555 F MG MG . A MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? metalc ? metalc4 A O THR 354 A THR 353 1_555 F MG MG . A MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc5 A OD1 ASN 629 A ASN 628 1_555 G MG MG . A MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc6 A OD1 ASP 704 A ASP 703 1_555 F MG MG . A MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc7 A O LEU 712 A LEU 711 1_555 H K K . A K 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.714 ? metalc ? metalc8 A O LYS 713 A LYS 712 1_555 H K K . A K 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.282 ? metalc ? metalc9 A O ALA 715 A ALA 714 1_555 H K K . A K 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.898 ? metalc ? metalc10 A OE2 GLU 733 A GLU 732 1_555 H K K . A K 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.801 ? metalc ? metalc11 A OE1 GLU 733 A GLU 732 1_555 H K K . A K 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.854 ? metalc ? metalc12 D O2 VN4 . A VN4 1001 1_555 F MG MG . A MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc13 D V VN4 . A VN4 1001 1_555 Q O HOH . A HOH 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc14 E O3G 128 . A 128 1002 1_555 G MG MG . A MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.436 ? metalc ? metalc15 E O2B 128 . A 128 1002 1_555 G MG MG . A MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc16 F MG MG . A MG 1003 1_555 Q O HOH . A HOH 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.874 ? metalc ? metalc17 F MG MG . A MG 1003 1_555 Q O HOH . A HOH 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc18 G MG MG . A MG 1004 1_555 Q O HOH . A HOH 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc19 B OE1 GLN 245 B GLN 244 1_555 O K K . B K 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.794 ? metalc ? metalc20 B OD1 ASP 352 B ASP 351 1_555 K V VN4 . B VN4 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc21 B OD2 ASP 352 B ASP 351 1_555 M MG MG . B MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc22 B O THR 354 B THR 353 1_555 M MG MG . B MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc23 B OD1 ASN 629 B ASN 628 1_555 N MG MG . B MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc24 B OD1 ASP 704 B ASP 703 1_555 M MG MG . B MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc25 B O LEU 712 B LEU 711 1_555 O K K . B K 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.79 ? metalc ? metalc26 B O LYS 713 B LYS 712 1_555 O K K . B K 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.319 ? metalc ? metalc27 B O ALA 715 B ALA 714 1_555 O K K . B K 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.809 ? metalc ? metalc28 B OE2 GLU 733 B GLU 732 1_555 O K K . B K 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.811 ? metalc ? metalc29 B OE1 GLU 733 B GLU 732 1_555 O K K . B K 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.786 ? metalc ? metalc30 K O2 VN4 . B VN4 1001 1_555 M MG MG . B MG 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? metalc ? metalc31 K V VN4 . B VN4 1001 1_555 R O HOH . B HOH 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? metalc ? metalc32 L O3G 128 . B 128 1002 1_555 N MG MG . B MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.969 ? metalc ? metalc33 L O2B 128 . B 128 1002 1_555 N MG MG . B MG 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc34 M MG MG . B MG 1003 1_555 R O HOH . B HOH 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? metalc ? metalc35 M MG MG . B MG 1003 1_555 R O HOH . B HOH 2003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc36 N MG MG . B MG 1004 1_555 R O HOH . B HOH 2004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? # _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 5A3S _atom_sites.fract_transf_matrix[1][1] 0.00766 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00238 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010663 _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] 0.007717 _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 TG1 A 1 1000 1000 TG1 TG1 . D 3 VN4 A 1 1001 1001 VN4 VN4 . E 4 128 A 1 1002 1002 128 128 . F 5 MG A 1 1003 1003 MG MG . G 5 MG A 1 1004 1004 MG MG . H 6 K A 1 1008 1008 K K . I 7 CL A 1 1009 1009 CL CL . J 2 TG1 B 1 1000 1000 TG1 TG1 . K 3 VN4 B 1 1001 1001 VN4 VN4 . L 4 128 B 1 1002 1002 128 128 . M 5 MG B 1 1003 1003 MG MG . N 5 MG B 1 1004 1004 MG MG . O 6 K B 1 1008 1008 K K . P 7 CL B 1 1009 1009 CL CL . Q 8 HOH A 1 2001 2001 HOH HOH . Q 8 HOH A 2 2002 2002 HOH HOH . Q 8 HOH A 3 2003 2003 HOH HOH . Q 8 HOH A 4 2004 2004 HOH HOH . R 8 HOH B 1 2001 2001 HOH HOH . R 8 HOH B 2 2002 2002 HOH HOH . R 8 HOH B 3 2003 2003 HOH HOH . R 8 HOH B 4 2004 2004 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 . . . L 4 52.819 21.176 39.462 1 203.2 ? PG 128 1002 B 1 HETATM 2 O O1G 128 . . . L 4 51.831 21.899 38.434 1 202.2 ? O1G 128 1002 B 1 HETATM 3 O O2G 128 . . . L 4 53.959 20.471 38.596 1 206.66 ? O2G 128 1002 B 1 HETATM 4 O O3G 128 . . . L 4 52.031 20.164 40.145 1 206.57 ? O3G 128 1002 B 1 HETATM 5 P PB 128 . . . L 4 53.23 22.993 41.695 1 201.23 ? PB 128 1002 B 1 HETATM 6 O O1B 128 . . . L 4 54.457 23.6 42.4 1 193.34 ? O1B 128 1002 B 1 HETATM 7 O O2B 128 . . . L 4 52.433 22.086 42.607 1 205.07 ? O2B 128 1002 B 1 HETATM 8 O O3B 128 . . . L 4 53.644 22.176 40.398 1 204.25 ? O3B 128 1002 B 1 HETATM 9 P PA 128 . . . L 4 52.886 25.69 40.519 1 201.44 ? PA 128 1002 B 1 HETATM 10 O O1A 128 . . . L 4 54.195 25.479 39.65 1 200.6 ? O1A 128 1002 B 1 HETATM 11 O O2A 128 . . . L 4 51.631 26.163 39.818 1 194.33 ? O2A 128 1002 B 1 HETATM 12 O O3A 128 . . . L 4 52.443 24.24 41.12 1 208.94 ? O3A 128 1002 B 1 HETATM 13 O O5' 128 . . . L 4 53.186 26.585 41.893 1 194.99 ? O5' 128 1002 B 1 HETATM 14 C C5' 128 . . . L 4 52.326 27.72 42.183 1 187.23 ? C5' 128 1002 B 1 HETATM 15 C C4' 128 . . . L 4 52.358 28.164 43.629 1 187.3 ? C4' 128 1002 B 1 HETATM 16 O O4' 128 . . . L 4 51.031 27.867 44.221 1 190.32 ? O4' 128 1002 B 1 HETATM 17 C C3' 128 . . . L 4 53.418 27.655 44.592 1 189.18 ? C3' 128 1002 B 1 HETATM 18 O O3' 128 . . . L 4 54.205 28.75 45.076 1 188.13 ? O3' 128 1002 B 1 HETATM 19 C C2' 128 . . . L 4 52.638 27.106 45.79 1 191.27 ? C2' 128 1002 B 1 HETATM 20 O O2' 128 . . . L 4 53.004 27.948 46.894 1 191.31 ? O2' 128 1002 B 1 HETATM 21 C C1' 128 . . . L 4 51.123 27.252 45.471 1 191.33 ? C1' 128 1002 B 1 HETATM 22 N N9 128 . . . L 4 50.42 26.02 45.329 1 191.09 ? N9 128 1002 B 1 HETATM 23 C C8 128 . . . L 4 50.288 25.265 44.202 1 199.03 ? C8 128 1002 B 1 HETATM 24 N N7 128 . . . L 4 49.59 24.179 44.353 1 193.67 ? N7 128 1002 B 1 HETATM 25 C C5 128 . . . L 4 49.224 24.207 45.694 1 182.32 ? C5 128 1002 B 1 HETATM 26 C C6 128 . . . L 4 48.449 23.314 46.522 1 168.85 ? C6 128 1002 B 1 HETATM 27 N N6 128 . . . L 4 47.892 22.171 46.063 1 153.56 ? N6 128 1002 B 1 HETATM 28 N N1 128 . . . L 4 48.282 23.655 47.819 1 166.69 ? N1 128 1002 B 1 HETATM 29 C C2 128 . . . L 4 48.841 24.785 48.256 1 162.31 ? C2 128 1002 B 1 HETATM 30 N N3 128 . . . L 4 49.572 25.689 47.601 1 165.48 ? N3 128 1002 B 1 HETATM 31 C C4 128 . . . L 4 49.736 25.349 46.312 1 178.69 ? C4 128 1002 B 1 HETATM 32 C C1F 128 . . . L 4 53.972 28.906 46.472 1 184.01 ? C1F 128 1002 B 1 HETATM 33 C C2F 128 . . . L 4 55.244 28.603 47.262 1 175.19 ? C2F 128 1002 B 1 HETATM 34 C C3F 128 . . . L 4 55.887 29.52 48.028 1 167.13 ? C3F 128 1002 B 1 HETATM 35 C C4F 128 . . . L 4 55.484 30.829 48.202 1 171.72 ? C4F 128 1002 B 1 HETATM 36 C C5F 128 . . . L 4 54.395 31.257 47.594 1 170.81 ? C5F 128 1002 B 1 HETATM 37 C C6F 128 . . . L 4 53.543 30.38 46.713 1 177.31 ? C6F 128 1002 B 1 HETATM 38 N N2F 128 . . . L 4 55.859 27.285 47.234 1 174.98 ? N2F 128 1002 B 1 HETATM 39 N N4F 128 . . . L 4 56.23 31.731 49.033 1 183.91 ? N4F 128 1002 B 1 HETATM 40 N N6F 128 . . . L 4 52.307 30.99 46.05 1 179.01 ? N6F 128 1002 B 1 HETATM 41 O O2F 128 . . . L 4 56.854 27.126 47.87 1 170.82 ? O2F 128 1002 B 1 HETATM 42 O O3F 128 . . . L 4 55.353 26.395 46.571 1 175.48 ? O3F 128 1002 B 1 HETATM 43 O O4F 128 . . . L 4 55.813 32.877 49.141 1 186.11 ? O4F 128 1002 B 1 HETATM 44 O O5F 128 . . . L 4 57.227 31.315 49.582 1 190.26 ? O5F 128 1002 B 1 HETATM 45 O O6F 128 . . . L 4 52.036 32.158 46.268 1 178.97 ? O6F 128 1002 B 1 HETATM 46 O O7F 128 . . . L 4 51.623 30.293 45.336 1 177.46 ? O7F 128 1002 B 1 # _model_server_stats.io_time_ms 37 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 46 #