data_1KY5 # _model_server_result.job_id 1zkitY2psaiDr4oeKgxjsg _model_server_result.datetime_utc '2024-12-01 19:16:05' _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 1ky5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":1433}' # _entry.id 1KY5 # _exptl.entry_id 1KY5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 265.225 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "3'-OXO-ADENOSINE" _entity.pdbx_number_of_molecules 4 _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 1KY5 _cell.length_a 91 _cell.length_b 223 _cell.length_c 91.2 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KY5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,E,F,G,H,I,J,K,L,M,N,O,P _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 F N N ? 3 H N N ? 3 J N N ? 3 L N N # _chem_comp.formula 'C10 H11 N5 O4' _chem_comp.formula_weight 265.225 _chem_comp.id ADY _chem_comp.mon_nstd_flag . _chem_comp.name "3'-OXO-ADENOSINE" _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 O5' C5' ADY sing 1 n n O5' HO5' ADY sing 2 n n C5' C4' ADY sing 3 n n C5' "H5'1" ADY sing 4 n n C5' "H5'2" ADY sing 5 n n C4' O4' ADY sing 6 n n C4' C3' ADY sing 7 n n C4' H4' ADY sing 8 n n O4' C1' ADY sing 9 n n C3' O3' ADY doub 10 n n C3' C2' ADY sing 11 n n C2' O2' ADY sing 12 n n C2' C1' ADY sing 13 n n C2' H2' ADY sing 14 n n O2' HO2' ADY sing 15 n n C1' N9 ADY sing 16 n n C1' H1' ADY sing 17 n n N9 C8 ADY sing 18 n y N9 C4 ADY sing 19 n y C8 N7 ADY doub 20 n y C8 H8 ADY sing 21 n n N7 C5 ADY sing 22 n y C5 C6 ADY sing 23 n y C5 C4 ADY doub 24 n y C6 N6 ADY sing 25 n n C6 N1 ADY doub 26 n y N6 HN61 ADY sing 27 n n N6 HN62 ADY sing 28 n n N1 C2 ADY sing 29 n y C2 N3 ADY doub 30 n y C2 H2 ADY sing 31 n n N3 C4 ADY sing 32 n y # _atom_sites.entry_id 1KY5 _atom_sites.fract_transf_matrix[1][1] 0.010989 _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] 0.004484 _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] 0.010965 _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 2 NAI A 1 432 432 NAI NAD . F 3 ADY A 1 433 433 ADY ADN . G 2 NAI B 1 1432 1432 NAI NAD . H 3 ADY B 1 1433 1433 ADY ADN . I 2 NAI C 1 2432 2432 NAI NAD . J 3 ADY C 1 2433 2433 ADY ADN . K 2 NAI D 1 3432 3432 NAI NAD . L 3 ADY D 1 3433 3433 ADY ADN . M 4 HOH A 1 5002 5002 HOH H2O . M 4 HOH A 2 5004 5004 HOH H2O . M 4 HOH A 3 5005 5005 HOH H2O . M 4 HOH A 4 5007 5007 HOH H2O . M 4 HOH A 5 5010 5010 HOH H2O . M 4 HOH A 6 5021 5021 HOH H2O . M 4 HOH A 7 5027 5027 HOH H2O . M 4 HOH A 8 5033 5033 HOH H2O . M 4 HOH A 9 5038 5038 HOH H2O . M 4 HOH A 10 5044 5044 HOH H2O . M 4 HOH A 11 5047 5047 HOH H2O . M 4 HOH A 12 5048 5048 HOH H2O . M 4 HOH A 13 5052 5052 HOH H2O . M 4 HOH A 14 5053 5053 HOH H2O . M 4 HOH A 15 5056 5056 HOH H2O . M 4 HOH A 16 5057 5057 HOH H2O . M 4 HOH A 17 5061 5061 HOH H2O . M 4 HOH A 18 5069 5069 HOH H2O . M 4 HOH A 19 5074 5074 HOH H2O . M 4 HOH A 20 5075 5075 HOH H2O . M 4 HOH A 21 5077 5077 HOH H2O . M 4 HOH A 22 5080 5080 HOH H2O . M 4 HOH A 23 5082 5082 HOH H2O . M 4 HOH A 24 5084 5084 HOH H2O . M 4 HOH A 25 5088 5088 HOH H2O . M 4 HOH A 26 5095 5095 HOH H2O . M 4 HOH A 27 5097 5097 HOH H2O . M 4 HOH A 28 5098 5098 HOH H2O . M 4 HOH A 29 5101 5101 HOH H2O . M 4 HOH A 30 5103 5103 HOH H2O . M 4 HOH A 31 5107 5107 HOH H2O . M 4 HOH A 32 5111 5111 HOH H2O . M 4 HOH A 33 5112 5112 HOH H2O . M 4 HOH A 34 5115 5115 HOH H2O . M 4 HOH A 35 5119 5119 HOH H2O . M 4 HOH A 36 5121 5121 HOH H2O . M 4 HOH A 37 5122 5122 HOH H2O . M 4 HOH A 38 5132 5132 HOH H2O . M 4 HOH A 39 5134 5134 HOH H2O . M 4 HOH A 40 5141 5141 HOH H2O . M 4 HOH A 41 5143 5143 HOH H2O . M 4 HOH A 42 5144 5144 HOH H2O . M 4 HOH A 43 5148 5148 HOH H2O . M 4 HOH A 44 5152 5152 HOH H2O . M 4 HOH A 45 5154 5154 HOH H2O . M 4 HOH A 46 5155 5155 HOH H2O . M 4 HOH A 47 5157 5157 HOH H2O . M 4 HOH A 48 5159 5159 HOH H2O . M 4 HOH A 49 5162 5162 HOH H2O . M 4 HOH A 50 5165 5165 HOH H2O . M 4 HOH A 51 5166 5166 HOH H2O . M 4 HOH A 52 5167 5167 HOH H2O . M 4 HOH A 53 5168 5168 HOH H2O . M 4 HOH A 54 5175 5175 HOH H2O . M 4 HOH A 55 5177 5177 HOH H2O . M 4 HOH A 56 5178 5178 HOH H2O . M 4 HOH A 57 5180 5180 HOH H2O . M 4 HOH A 58 5185 5185 HOH H2O . M 4 HOH A 59 5187 5187 HOH H2O . M 4 HOH A 60 5188 5188 HOH H2O . M 4 HOH A 61 5189 5189 HOH H2O . M 4 HOH A 62 5196 5196 HOH H2O . M 4 HOH A 63 5199 5199 HOH H2O . M 4 HOH A 64 5201 5201 HOH H2O . M 4 HOH A 65 5205 5205 HOH H2O . M 4 HOH A 66 5206 5206 HOH H2O . M 4 HOH A 67 5213 5213 HOH H2O . M 4 HOH A 68 5219 5219 HOH H2O . M 4 HOH A 69 5222 5222 HOH H2O . M 4 HOH A 70 5223 5223 HOH H2O . M 4 HOH A 71 5227 5227 HOH H2O . M 4 HOH A 72 5228 5228 HOH H2O . M 4 HOH A 73 5229 5229 HOH H2O . M 4 HOH A 74 5235 5235 HOH H2O . M 4 HOH A 75 5242 5242 HOH H2O . M 4 HOH A 76 5246 5246 HOH H2O . M 4 HOH A 77 5247 5247 HOH H2O . M 4 HOH A 78 5249 5249 HOH H2O . M 4 HOH A 79 5250 5250 HOH H2O . N 4 HOH B 1 5001 5001 HOH H2O . N 4 HOH B 2 5003 5003 HOH H2O . N 4 HOH B 3 5006 5006 HOH H2O . N 4 HOH B 4 5011 5011 HOH H2O . N 4 HOH B 5 5014 5014 HOH H2O . N 4 HOH B 6 5019 5019 HOH H2O . N 4 HOH B 7 5022 5022 HOH H2O . N 4 HOH B 8 5023 5023 HOH H2O . N 4 HOH B 9 5024 5024 HOH H2O . N 4 HOH B 10 5025 5025 HOH H2O . N 4 HOH B 11 5026 5026 HOH H2O . N 4 HOH B 12 5035 5035 HOH H2O . N 4 HOH B 13 5037 5037 HOH H2O . N 4 HOH B 14 5039 5039 HOH H2O . N 4 HOH B 15 5040 5040 HOH H2O . N 4 HOH B 16 5042 5042 HOH H2O . N 4 HOH B 17 5043 5043 HOH H2O . N 4 HOH B 18 5049 5049 HOH H2O . N 4 HOH B 19 5051 5051 HOH H2O . N 4 HOH B 20 5054 5054 HOH H2O . N 4 HOH B 21 5058 5058 HOH H2O . N 4 HOH B 22 5059 5059 HOH H2O . N 4 HOH B 23 5062 5062 HOH H2O . N 4 HOH B 24 5063 5063 HOH H2O . N 4 HOH B 25 5065 5065 HOH H2O . N 4 HOH B 26 5066 5066 HOH H2O . N 4 HOH B 27 5068 5068 HOH H2O . N 4 HOH B 28 5081 5081 HOH H2O . N 4 HOH B 29 5085 5085 HOH H2O . N 4 HOH B 30 5086 5086 HOH H2O . N 4 HOH B 31 5090 5090 HOH H2O . N 4 HOH B 32 5092 5092 HOH H2O . N 4 HOH B 33 5104 5104 HOH H2O . N 4 HOH B 34 5105 5105 HOH H2O . N 4 HOH B 35 5109 5109 HOH H2O . N 4 HOH B 36 5113 5113 HOH H2O . N 4 HOH B 37 5123 5123 HOH H2O . N 4 HOH B 38 5127 5127 HOH H2O . N 4 HOH B 39 5128 5128 HOH H2O . N 4 HOH B 40 5129 5129 HOH H2O . N 4 HOH B 41 5137 5137 HOH H2O . N 4 HOH B 42 5139 5139 HOH H2O . N 4 HOH B 43 5142 5142 HOH H2O . N 4 HOH B 44 5146 5146 HOH H2O . N 4 HOH B 45 5147 5147 HOH H2O . N 4 HOH B 46 5150 5150 HOH H2O . N 4 HOH B 47 5153 5153 HOH H2O . N 4 HOH B 48 5161 5161 HOH H2O . N 4 HOH B 49 5163 5163 HOH H2O . N 4 HOH B 50 5169 5169 HOH H2O . N 4 HOH B 51 5170 5170 HOH H2O . N 4 HOH B 52 5171 5171 HOH H2O . N 4 HOH B 53 5172 5172 HOH H2O . N 4 HOH B 54 5173 5173 HOH H2O . N 4 HOH B 55 5192 5192 HOH H2O . N 4 HOH B 56 5195 5195 HOH H2O . N 4 HOH B 57 5202 5202 HOH H2O . N 4 HOH B 58 5209 5209 HOH H2O . N 4 HOH B 59 5211 5211 HOH H2O . N 4 HOH B 60 5220 5220 HOH H2O . N 4 HOH B 61 5225 5225 HOH H2O . N 4 HOH B 62 5230 5230 HOH H2O . N 4 HOH B 63 5231 5231 HOH H2O . N 4 HOH B 64 5234 5234 HOH H2O . N 4 HOH B 65 5236 5236 HOH H2O . N 4 HOH B 66 5238 5238 HOH H2O . N 4 HOH B 67 5240 5240 HOH H2O . N 4 HOH B 68 5244 5244 HOH H2O . O 4 HOH C 1 5009 5009 HOH H2O . O 4 HOH C 2 5017 5017 HOH H2O . O 4 HOH C 3 5018 5018 HOH H2O . O 4 HOH C 4 5020 5020 HOH H2O . O 4 HOH C 5 5028 5028 HOH H2O . O 4 HOH C 6 5032 5032 HOH H2O . O 4 HOH C 7 5034 5034 HOH H2O . O 4 HOH C 8 5036 5036 HOH H2O . O 4 HOH C 9 5050 5050 HOH H2O . O 4 HOH C 10 5060 5060 HOH H2O . O 4 HOH C 11 5067 5067 HOH H2O . O 4 HOH C 12 5070 5070 HOH H2O . O 4 HOH C 13 5073 5073 HOH H2O . O 4 HOH C 14 5079 5079 HOH H2O . O 4 HOH C 15 5093 5093 HOH H2O . O 4 HOH C 16 5094 5094 HOH H2O . O 4 HOH C 17 5106 5106 HOH H2O . O 4 HOH C 18 5108 5108 HOH H2O . O 4 HOH C 19 5110 5110 HOH H2O . O 4 HOH C 20 5114 5114 HOH H2O . O 4 HOH C 21 5118 5118 HOH H2O . O 4 HOH C 22 5124 5124 HOH H2O . O 4 HOH C 23 5125 5125 HOH H2O . O 4 HOH C 24 5126 5126 HOH H2O . O 4 HOH C 25 5130 5130 HOH H2O . O 4 HOH C 26 5131 5131 HOH H2O . O 4 HOH C 27 5138 5138 HOH H2O . O 4 HOH C 28 5140 5140 HOH H2O . O 4 HOH C 29 5145 5145 HOH H2O . O 4 HOH C 30 5160 5160 HOH H2O . O 4 HOH C 31 5164 5164 HOH H2O . O 4 HOH C 32 5174 5174 HOH H2O . O 4 HOH C 33 5176 5176 HOH H2O . O 4 HOH C 34 5190 5190 HOH H2O . O 4 HOH C 35 5197 5197 HOH H2O . O 4 HOH C 36 5200 5200 HOH H2O . O 4 HOH C 37 5203 5203 HOH H2O . O 4 HOH C 38 5204 5204 HOH H2O . O 4 HOH C 39 5207 5207 HOH H2O . O 4 HOH C 40 5208 5208 HOH H2O . O 4 HOH C 41 5212 5212 HOH H2O . O 4 HOH C 42 5214 5214 HOH H2O . O 4 HOH C 43 5217 5217 HOH H2O . O 4 HOH C 44 5218 5218 HOH H2O . O 4 HOH C 45 5221 5221 HOH H2O . O 4 HOH C 46 5224 5224 HOH H2O . O 4 HOH C 47 5226 5226 HOH H2O . O 4 HOH C 48 5233 5233 HOH H2O . O 4 HOH C 49 5237 5237 HOH H2O . O 4 HOH C 50 5241 5241 HOH H2O . O 4 HOH C 51 5243 5243 HOH H2O . O 4 HOH C 52 5245 5245 HOH H2O . O 4 HOH C 53 5251 5251 HOH H2O . O 4 HOH C 54 5252 5252 HOH H2O . P 4 HOH D 1 5008 5008 HOH H2O . P 4 HOH D 2 5012 5012 HOH H2O . P 4 HOH D 3 5013 5013 HOH H2O . P 4 HOH D 4 5015 5015 HOH H2O . P 4 HOH D 5 5016 5016 HOH H2O . P 4 HOH D 6 5029 5029 HOH H2O . P 4 HOH D 7 5030 5030 HOH H2O . P 4 HOH D 8 5031 5031 HOH H2O . P 4 HOH D 9 5041 5041 HOH H2O . P 4 HOH D 10 5045 5045 HOH H2O . P 4 HOH D 11 5046 5046 HOH H2O . P 4 HOH D 12 5055 5055 HOH H2O . P 4 HOH D 13 5064 5064 HOH H2O . P 4 HOH D 14 5071 5071 HOH H2O . P 4 HOH D 15 5072 5072 HOH H2O . P 4 HOH D 16 5076 5076 HOH H2O . P 4 HOH D 17 5078 5078 HOH H2O . P 4 HOH D 18 5083 5083 HOH H2O . P 4 HOH D 19 5087 5087 HOH H2O . P 4 HOH D 20 5089 5089 HOH H2O . P 4 HOH D 21 5091 5091 HOH H2O . P 4 HOH D 22 5096 5096 HOH H2O . P 4 HOH D 23 5099 5099 HOH H2O . P 4 HOH D 24 5100 5100 HOH H2O . P 4 HOH D 25 5102 5102 HOH H2O . P 4 HOH D 26 5116 5116 HOH H2O . P 4 HOH D 27 5117 5117 HOH H2O . P 4 HOH D 28 5120 5120 HOH H2O . P 4 HOH D 29 5133 5133 HOH H2O . P 4 HOH D 30 5135 5135 HOH H2O . P 4 HOH D 31 5136 5136 HOH H2O . P 4 HOH D 32 5149 5149 HOH H2O . P 4 HOH D 33 5151 5151 HOH H2O . P 4 HOH D 34 5156 5156 HOH H2O . P 4 HOH D 35 5158 5158 HOH H2O . P 4 HOH D 36 5179 5179 HOH H2O . P 4 HOH D 37 5181 5181 HOH H2O . P 4 HOH D 38 5182 5182 HOH H2O . P 4 HOH D 39 5183 5183 HOH H2O . P 4 HOH D 40 5184 5184 HOH H2O . P 4 HOH D 41 5186 5186 HOH H2O . P 4 HOH D 42 5191 5191 HOH H2O . P 4 HOH D 43 5193 5193 HOH H2O . P 4 HOH D 44 5194 5194 HOH H2O . P 4 HOH D 45 5198 5198 HOH H2O . P 4 HOH D 46 5210 5210 HOH H2O . P 4 HOH D 47 5215 5215 HOH H2O . P 4 HOH D 48 5216 5216 HOH H2O . P 4 HOH D 49 5232 5232 HOH H2O . P 4 HOH D 50 5239 5239 HOH H2O . P 4 HOH D 51 5248 5248 HOH H2O . # 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 O O5' ADY . . . H 3 10.988 24.993 49.429 1 2 ? O5' ADY 1433 B 1 HETATM 2 C C5' ADY . . . H 3 12.316 25.162 48.953 1 4.17 ? C5' ADY 1433 B 1 HETATM 3 C C4' ADY . . . H 3 12.673 23.77 48.476 1 9.09 ? C4' ADY 1433 B 1 HETATM 4 O O4' ADY . . . H 3 11.864 23.368 47.329 1 15.93 ? O4' ADY 1433 B 1 HETATM 5 C C3' ADY . . . H 3 14.032 23.28 48.14 1 12.91 ? C3' ADY 1433 B 1 HETATM 6 O O3' ADY . . . H 3 14.964 23.333 48.969 1 20.66 ? O3' ADY 1433 B 1 HETATM 7 C C2' ADY . . . H 3 13.983 22.554 46.813 1 11.18 ? C2' ADY 1433 B 1 HETATM 8 O O2' ADY . . . H 3 14.93 21.497 46.968 1 12.56 ? O2' ADY 1433 B 1 HETATM 9 C C1' ADY . . . H 3 12.5 22.167 46.93 1 12 ? C1' ADY 1433 B 1 HETATM 10 N N9 ADY . . . H 3 11.896 21.554 45.71 1 10.06 ? N9 ADY 1433 B 1 HETATM 11 C C8 ADY . . . H 3 11.978 22.019 44.376 1 10.76 ? C8 ADY 1433 B 1 HETATM 12 N N7 ADY . . . H 3 11.347 21.275 43.489 1 9.91 ? N7 ADY 1433 B 1 HETATM 13 C C5 ADY . . . H 3 10.803 20.246 44.265 1 11.28 ? C5 ADY 1433 B 1 HETATM 14 C C6 ADY . . . H 3 9.998 19.083 43.953 1 12.62 ? C6 ADY 1433 B 1 HETATM 15 N N6 ADY . . . H 3 9.601 18.776 42.725 1 17.84 ? N6 ADY 1433 B 1 HETATM 16 N N1 ADY . . . H 3 9.636 18.27 44.986 1 13.06 ? N1 ADY 1433 B 1 HETATM 17 C C2 ADY . . . H 3 10.03 18.562 46.25 1 13.31 ? C2 ADY 1433 B 1 HETATM 18 N N3 ADY . . . H 3 10.779 19.603 46.674 1 11.65 ? N3 ADY 1433 B 1 HETATM 19 C C4 ADY . . . H 3 11.134 20.408 45.632 1 13.43 ? C4 ADY 1433 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 229 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 19 #