data_5EKV # _model_server_result.job_id f_HQ6wPSWMyOyvFmMY1JwQ _model_server_result.datetime_utc '2024-11-28 13:44:31' _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 5ekv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":301}' # _entry.id 5EKV # _exptl.entry_id 5EKV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 393.331 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]-4-oxidanyl-cyclobut-3-ene-1,2-dione _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 90 _cell.angle_gamma 90 _cell.entry_id 5EKV _cell.length_a 38.48 _cell.length_b 100.78 _cell.length_c 136.46 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5EKV _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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,B,E 1 1 C,D,F 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 ? 3 E N N ? 3 F N N # _chem_comp.formula 'C15 H17 N6 O7 1' _chem_comp.formula_weight 393.331 _chem_comp.id 5PQ _chem_comp.mon_nstd_flag . _chem_comp.name 3-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]-4-oxidanyl-cyclobut-3-ene-1,2-dione _chem_comp.type non-polymer _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 OAE CAT 5PQ doub 1 n n NAL CAQ 5PQ sing 2 n n NAL CAJ 5PQ sing 3 n n N2 C2 5PQ sing 4 n n N1 C2 5PQ sing 5 n n N1 C6 5PQ sing 6 n n O6 C6 5PQ doub 7 n n C2 N3 5PQ doub 8 n n CAT CAQ 5PQ sing 9 n n CAT CAS 5PQ sing 10 n n C6 C5 5PQ sing 11 n n OAN CAY 5PQ sing 12 n n OAN CAZ 5PQ sing 13 n n N3 C4 5PQ sing 14 n n CAQ CAP 5PQ doub 15 n n C5 C4 5PQ doub 16 n y C5 N7 5PQ sing 17 n y CAJ CAY 5PQ sing 18 n n C4 N9 5PQ sing 19 n y CAA N7 5PQ sing 20 n n N7 C8 5PQ doub 21 n y N9 C8 5PQ sing 22 n y N9 CAZ 5PQ sing 23 n n CAY CAW 5PQ sing 24 n n CAZ CAX 5PQ sing 25 n n CAS CAP 5PQ sing 26 n n CAS OAD 5PQ doub 27 n n CAP OAF 5PQ sing 28 n n CAW CAX 5PQ sing 29 n n CAW OAG 5PQ sing 30 n n CAX OAH 5PQ sing 31 n n C8 H1 5PQ sing 32 n n N1 H2 5PQ sing 33 n n N2 H3 5PQ sing 34 n n N2 H4 5PQ sing 35 n n CAA H5 5PQ sing 36 n n CAA H6 5PQ sing 37 n n CAA H7 5PQ sing 38 n n CAZ H8 5PQ sing 39 n n CAX H9 5PQ sing 40 n n OAH H10 5PQ sing 41 n n CAW H11 5PQ sing 42 n n OAG H12 5PQ sing 43 n n CAY H13 5PQ sing 44 n n CAJ H14 5PQ sing 45 n n CAJ H15 5PQ sing 46 n n NAL H16 5PQ sing 47 n n OAF H17 5PQ sing 48 n n # _atom_sites.entry_id 5EKV _atom_sites.fract_transf_matrix[1][1] 0.025988 _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] 0.009923 _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] 0.007328 _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 E 3 5PQ A 1 301 1 5PQ DRG . F 3 5PQ C 1 301 1 5PQ DRG . # 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 C C4 5PQ . . . F 3 12.983 -44.147 56.345 0.74 24.66 ? C4 5PQ 301 C 1 HETATM 2 C C5 5PQ . . . F 3 11.974 -43.858 55.439 0.74 24.63 ? C5 5PQ 301 C 1 HETATM 3 C C6 5PQ . . . F 3 11.101 -44.854 55.027 0.74 24.51 ? C6 5PQ 301 C 1 HETATM 4 C C8 5PQ . . . F 3 13.113 -42.046 55.825 0.74 24.85 ? C8 5PQ 301 C 1 HETATM 5 N N1 5PQ . . . F 3 11.265 -46.141 55.543 0.74 24.62 ? N1 5PQ 301 C 1 HETATM 6 N N2 5PQ . . . F 3 12.468 -47.603 56.957 0.74 25.07 ? N2 5PQ 301 C 1 HETATM 7 N N3 5PQ . . . F 3 13.124 -45.39 56.831 0.74 24.76 ? N3 5PQ 301 C 1 HETATM 8 O O6 5PQ . . . F 3 10.203 -44.61 54.223 0.74 24.17 ? O6 5PQ 301 C 1 HETATM 9 C C2 5PQ . . . F 3 12.3 -46.382 56.457 0.74 24.89 ? C2 5PQ 301 C 1 HETATM 10 N N7 5PQ . . . F 3 12.093 -42.57 55.152 0.74 24.61 ? N7 5PQ 301 C 1 HETATM 11 C CAA 5PQ . . . F 3 11.219 -41.824 54.22 0.74 23.9 ? CAA 5PQ 301 C 1 HETATM 12 N N9 5PQ . . . F 3 13.659 -43.018 56.559 0.74 24.93 ? N9 5PQ 301 C 1 HETATM 13 C CAZ 5PQ . . . F 3 14.824 -42.867 57.46 0.74 25.12 ? CAZ 5PQ 301 C 1 HETATM 14 O OAN 5PQ . . . F 3 15.103 -41.472 57.653 0.74 24.95 ? OAN 5PQ 301 C 1 HETATM 15 C CAX 5PQ . . . F 3 16.078 -43.404 56.769 0.74 24.95 ? CAX 5PQ 301 C 1 HETATM 16 O OAH 5PQ . . . F 3 16.362 -44.72 57.25 0.74 25.11 ? OAH 5PQ 301 C 1 HETATM 17 C CAW 5PQ . . . F 3 17.183 -42.446 57.218 0.74 24.84 ? CAW 5PQ 301 C 1 HETATM 18 O OAG 5PQ . . . F 3 18.157 -43.165 57.979 0.74 24.92 ? OAG 5PQ 301 C 1 HETATM 19 C CAY 5PQ . . . F 3 16.459 -41.45 58.125 0.74 24.53 ? CAY 5PQ 301 C 1 HETATM 20 C CAJ 5PQ . . . F 3 17.048 -40.052 57.922 0.74 23.91 ? CAJ 5PQ 301 C 1 HETATM 21 N NAL 5PQ . . . F 3 18.389 -39.993 58.521 0.74 23.59 ? NAL 5PQ 301 C 1 HETATM 22 C CAQ 5PQ . . . F 3 18.669 -38.738 58.86 0.74 22.97 ? CAQ 5PQ 301 C 1 HETATM 23 C CAT 5PQ . . . F 3 19.924 -37.863 58.828 0.74 22.44 ? CAT 5PQ 301 C 1 HETATM 24 O OAE 5PQ . . . F 3 21.091 -38.03 58.478 0.74 22.48 ? OAE 5PQ 301 C 1 HETATM 25 C CAS 5PQ . . . F 3 19.125 -36.696 59.411 0.74 22.2 ? CAS 5PQ 301 C 1 HETATM 26 O OAD 5PQ . . . F 3 19.384 -35.535 59.725 0.74 22.19 ? OAD 5PQ 301 C 1 HETATM 27 C CAP 5PQ . . . F 3 17.87 -37.571 59.443 0.74 22.16 ? CAP 5PQ 301 C 1 HETATM 28 O OAF 5PQ . . . F 3 16.579 -37.387 59.83 0.74 21.59 ? OAF 5PQ 301 C 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 278 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 28 #