data_2ZI5 # _model_server_result.job_id eUpYF7w46_p6QqasfOpu1A _model_server_result.datetime_utc '2024-11-13 05:28:21' _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 2zi5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":3401}' # _entry.id 2ZI5 # _exptl.entry_id 2ZI5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 251.242 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2S,3R,5S)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol _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 2ZI5 _cell.length_a 138.36 _cell.length_b 138.65 _cell.length_c 119.01 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2ZI5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 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 PISA dimeric 2 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,M,N 1 1 C,I,J,O 2 1,2 D,K,L,P 3 1,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 3_655 -x+1,y,-z+1/2 -1 0 0 0 1 0 0 0 -1 138.36 0 59.505 3 'crystal symmetry operation' 3_654 -x+1,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 138.36 0 -59.505 # 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 H13 N5 O3' _chem_comp.formula_weight 251.242 _chem_comp.id 3L1 _chem_comp.mon_nstd_flag . _chem_comp.name (2S,3R,5S)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "L-2'-deoxyadenosine" # 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 N6 C6 3L1 sing 1 n n C6 N1 3L1 doub 2 n y C6 C5 3L1 sing 3 n y N1 C2 3L1 sing 4 n y C2 N3 3L1 doub 5 n y N3 C4 3L1 sing 6 n y C4 C5 3L1 doub 7 n y C4 N9 3L1 sing 8 n y C5 N7 3L1 sing 9 n y N7 C8 3L1 doub 10 n y C8 N9 3L1 sing 11 n y N9 C1' 3L1 sing 12 n n C1' O4' 3L1 sing 13 n n C1' C2' 3L1 sing 14 n n O4' C4' 3L1 sing 15 n n C2' C3' 3L1 sing 16 n n C3' O3' 3L1 sing 17 n n C3' C4' 3L1 sing 18 n n C4' C5' 3L1 sing 19 n n C5' O5' 3L1 sing 20 n n N6 HN6 3L1 sing 21 n n N6 HN6A 3L1 sing 22 n n C2 H2 3L1 sing 23 n n C8 H8 3L1 sing 24 n n C1' H1' 3L1 sing 25 n n C2' H2' 3L1 sing 26 n n C2' "H2'A" 3L1 sing 27 n n C3' H3' 3L1 sing 28 n n O3' HO3' 3L1 sing 29 n n C4' H4' 3L1 sing 30 n n C5' H5' 3L1 sing 31 n n C5' "H5'A" 3L1 sing 32 n n O5' HO5' 3L1 sing 33 n n # _atom_sites.entry_id 2ZI5 _atom_sites.fract_transf_matrix[1][1] 0.007228 _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] 0.007212 _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] 0.008403 _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 UDP A 1 1301 1301 UDP UDP . F 3 3L1 A 1 1401 1401 3L1 LAD . G 2 UDP B 1 2301 2301 UDP UDP . H 3 3L1 B 1 2401 2401 3L1 LAD . I 2 UDP C 1 3301 3301 UDP UDP . J 3 3L1 C 1 3401 3401 3L1 LAD . K 2 UDP D 1 4301 4301 UDP UDP . L 3 3L1 D 1 4401 4401 3L1 LAD . M 4 HOH A 1 6004 6004 HOH HOH . M 4 HOH A 2 6005 6005 HOH HOH . M 4 HOH A 3 6012 6012 HOH HOH . M 4 HOH A 4 6015 6015 HOH HOH . M 4 HOH A 5 6018 6018 HOH HOH . M 4 HOH A 6 6023 6023 HOH HOH . M 4 HOH A 7 6029 6029 HOH HOH . M 4 HOH A 8 6032 6032 HOH HOH . M 4 HOH A 9 6037 6037 HOH HOH . M 4 HOH A 10 6064 6064 HOH HOH . M 4 HOH A 11 6098 6098 HOH HOH . M 4 HOH A 12 6102 6102 HOH HOH . M 4 HOH A 13 6104 6104 HOH HOH . M 4 HOH A 14 6110 6110 HOH HOH . M 4 HOH A 15 6118 6118 HOH HOH . M 4 HOH A 16 6119 6119 HOH HOH . M 4 HOH A 17 6134 6134 HOH HOH . M 4 HOH A 18 6135 6135 HOH HOH . M 4 HOH A 19 6136 6136 HOH HOH . M 4 HOH A 20 6137 6137 HOH HOH . M 4 HOH A 21 6138 6138 HOH HOH . M 4 HOH A 22 6144 6144 HOH HOH . M 4 HOH A 23 6156 6156 HOH HOH . M 4 HOH A 24 6164 6164 HOH HOH . M 4 HOH A 25 6171 6171 HOH HOH . M 4 HOH A 26 6174 6174 HOH HOH . M 4 HOH A 27 6175 6175 HOH HOH . M 4 HOH A 28 6177 6177 HOH HOH . M 4 HOH A 29 6178 6178 HOH HOH . M 4 HOH A 30 6179 6179 HOH HOH . M 4 HOH A 31 6180 6180 HOH HOH . M 4 HOH A 32 6181 6181 HOH HOH . M 4 HOH A 33 6183 6183 HOH HOH . M 4 HOH A 34 6184 6184 HOH HOH . M 4 HOH A 35 6185 6185 HOH HOH . M 4 HOH A 36 6204 6204 HOH HOH . M 4 HOH A 37 6205 6205 HOH HOH . M 4 HOH A 38 6206 6206 HOH HOH . M 4 HOH A 39 6207 6207 HOH HOH . M 4 HOH A 40 6208 6208 HOH HOH . M 4 HOH A 41 6209 6209 HOH HOH . M 4 HOH A 42 6214 6214 HOH HOH . M 4 HOH A 43 6223 6223 HOH HOH . N 4 HOH B 1 6001 6001 HOH HOH . N 4 HOH B 2 6003 6003 HOH HOH . N 4 HOH B 3 6009 6009 HOH HOH . N 4 HOH B 4 6011 6011 HOH HOH . N 4 HOH B 5 6020 6020 HOH HOH . N 4 HOH B 6 6024 6024 HOH HOH . N 4 HOH B 7 6027 6027 HOH HOH . N 4 HOH B 8 6028 6028 HOH HOH . N 4 HOH B 9 6030 6030 HOH HOH . N 4 HOH B 10 6031 6031 HOH HOH . N 4 HOH B 11 6033 6033 HOH HOH . N 4 HOH B 12 6034 6034 HOH HOH . N 4 HOH B 13 6036 6036 HOH HOH . N 4 HOH B 14 6038 6038 HOH HOH . N 4 HOH B 15 6040 6040 HOH HOH . N 4 HOH B 16 6049 6049 HOH HOH . N 4 HOH B 17 6052 6052 HOH HOH . N 4 HOH B 18 6053 6053 HOH HOH . N 4 HOH B 19 6055 6055 HOH HOH . N 4 HOH B 20 6056 6056 HOH HOH . N 4 HOH B 21 6057 6057 HOH HOH . N 4 HOH B 22 6058 6058 HOH HOH . N 4 HOH B 23 6059 6059 HOH HOH . N 4 HOH B 24 6060 6060 HOH HOH . N 4 HOH B 25 6061 6061 HOH HOH . N 4 HOH B 26 6062 6062 HOH HOH . N 4 HOH B 27 6063 6063 HOH HOH . N 4 HOH B 28 6066 6066 HOH HOH . N 4 HOH B 29 6067 6067 HOH HOH . N 4 HOH B 30 6068 6068 HOH HOH . N 4 HOH B 31 6069 6069 HOH HOH . N 4 HOH B 32 6070 6070 HOH HOH . N 4 HOH B 33 6071 6071 HOH HOH . N 4 HOH B 34 6072 6072 HOH HOH . N 4 HOH B 35 6073 6073 HOH HOH . N 4 HOH B 36 6080 6080 HOH HOH . N 4 HOH B 37 6116 6116 HOH HOH . N 4 HOH B 38 6120 6120 HOH HOH . N 4 HOH B 39 6122 6122 HOH HOH . N 4 HOH B 40 6123 6123 HOH HOH . N 4 HOH B 41 6124 6124 HOH HOH . N 4 HOH B 42 6125 6125 HOH HOH . N 4 HOH B 43 6126 6126 HOH HOH . N 4 HOH B 44 6139 6139 HOH HOH . N 4 HOH B 45 6140 6140 HOH HOH . N 4 HOH B 46 6141 6141 HOH HOH . N 4 HOH B 47 6142 6142 HOH HOH . N 4 HOH B 48 6145 6145 HOH HOH . N 4 HOH B 49 6157 6157 HOH HOH . N 4 HOH B 50 6158 6158 HOH HOH . N 4 HOH B 51 6159 6159 HOH HOH . N 4 HOH B 52 6165 6165 HOH HOH . N 4 HOH B 53 6166 6166 HOH HOH . N 4 HOH B 54 6167 6167 HOH HOH . N 4 HOH B 55 6168 6168 HOH HOH . N 4 HOH B 56 6176 6176 HOH HOH . N 4 HOH B 57 6186 6186 HOH HOH . N 4 HOH B 58 6188 6188 HOH HOH . N 4 HOH B 59 6189 6189 HOH HOH . N 4 HOH B 60 6190 6190 HOH HOH . N 4 HOH B 61 6191 6191 HOH HOH . N 4 HOH B 62 6192 6192 HOH HOH . N 4 HOH B 63 6193 6193 HOH HOH . N 4 HOH B 64 6195 6195 HOH HOH . N 4 HOH B 65 6196 6196 HOH HOH . N 4 HOH B 66 6197 6197 HOH HOH . N 4 HOH B 67 6198 6198 HOH HOH . N 4 HOH B 68 6213 6213 HOH HOH . N 4 HOH B 69 6221 6221 HOH HOH . N 4 HOH B 70 6222 6222 HOH HOH . N 4 HOH B 71 6224 6224 HOH HOH . O 4 HOH C 1 6008 6008 HOH HOH . O 4 HOH C 2 6013 6013 HOH HOH . O 4 HOH C 3 6014 6014 HOH HOH . O 4 HOH C 4 6019 6019 HOH HOH . O 4 HOH C 5 6035 6035 HOH HOH . O 4 HOH C 6 6039 6039 HOH HOH . O 4 HOH C 7 6041 6041 HOH HOH . O 4 HOH C 8 6042 6042 HOH HOH . O 4 HOH C 9 6043 6043 HOH HOH . O 4 HOH C 10 6044 6044 HOH HOH . O 4 HOH C 11 6045 6045 HOH HOH . O 4 HOH C 12 6050 6050 HOH HOH . O 4 HOH C 13 6051 6051 HOH HOH . O 4 HOH C 14 6065 6065 HOH HOH . O 4 HOH C 15 6074 6074 HOH HOH . O 4 HOH C 16 6075 6075 HOH HOH . O 4 HOH C 17 6076 6076 HOH HOH . O 4 HOH C 18 6077 6077 HOH HOH . O 4 HOH C 19 6078 6078 HOH HOH . O 4 HOH C 20 6079 6079 HOH HOH . O 4 HOH C 21 6081 6081 HOH HOH . O 4 HOH C 22 6082 6082 HOH HOH . O 4 HOH C 23 6083 6083 HOH HOH . O 4 HOH C 24 6084 6084 HOH HOH . O 4 HOH C 25 6086 6086 HOH HOH . O 4 HOH C 26 6087 6087 HOH HOH . O 4 HOH C 27 6088 6088 HOH HOH . O 4 HOH C 28 6089 6089 HOH HOH . O 4 HOH C 29 6090 6090 HOH HOH . O 4 HOH C 30 6091 6091 HOH HOH . O 4 HOH C 31 6092 6092 HOH HOH . O 4 HOH C 32 6093 6093 HOH HOH . O 4 HOH C 33 6094 6094 HOH HOH . O 4 HOH C 34 6095 6095 HOH HOH . O 4 HOH C 35 6096 6096 HOH HOH . O 4 HOH C 36 6097 6097 HOH HOH . O 4 HOH C 37 6099 6099 HOH HOH . O 4 HOH C 38 6114 6114 HOH HOH . O 4 HOH C 39 6117 6117 HOH HOH . O 4 HOH C 40 6121 6121 HOH HOH . O 4 HOH C 41 6128 6128 HOH HOH . O 4 HOH C 42 6129 6129 HOH HOH . O 4 HOH C 43 6131 6131 HOH HOH . O 4 HOH C 44 6133 6133 HOH HOH . O 4 HOH C 45 6147 6147 HOH HOH . O 4 HOH C 46 6149 6149 HOH HOH . O 4 HOH C 47 6150 6150 HOH HOH . O 4 HOH C 48 6153 6153 HOH HOH . O 4 HOH C 49 6154 6154 HOH HOH . O 4 HOH C 50 6160 6160 HOH HOH . O 4 HOH C 51 6161 6161 HOH HOH . O 4 HOH C 52 6170 6170 HOH HOH . O 4 HOH C 53 6172 6172 HOH HOH . O 4 HOH C 54 6173 6173 HOH HOH . O 4 HOH C 55 6194 6194 HOH HOH . O 4 HOH C 56 6199 6199 HOH HOH . O 4 HOH C 57 6202 6202 HOH HOH . O 4 HOH C 58 6203 6203 HOH HOH . O 4 HOH C 59 6210 6210 HOH HOH . O 4 HOH C 60 6211 6211 HOH HOH . O 4 HOH C 61 6212 6212 HOH HOH . O 4 HOH C 62 6215 6215 HOH HOH . P 4 HOH D 1 6002 6002 HOH HOH . P 4 HOH D 2 6006 6006 HOH HOH . P 4 HOH D 3 6007 6007 HOH HOH . P 4 HOH D 4 6010 6010 HOH HOH . P 4 HOH D 5 6016 6016 HOH HOH . P 4 HOH D 6 6017 6017 HOH HOH . P 4 HOH D 7 6021 6021 HOH HOH . P 4 HOH D 8 6022 6022 HOH HOH . P 4 HOH D 9 6025 6025 HOH HOH . P 4 HOH D 10 6026 6026 HOH HOH . P 4 HOH D 11 6047 6047 HOH HOH . P 4 HOH D 12 6048 6048 HOH HOH . P 4 HOH D 13 6100 6100 HOH HOH . P 4 HOH D 14 6101 6101 HOH HOH . P 4 HOH D 15 6103 6103 HOH HOH . P 4 HOH D 16 6105 6105 HOH HOH . P 4 HOH D 17 6106 6106 HOH HOH . P 4 HOH D 18 6107 6107 HOH HOH . P 4 HOH D 19 6108 6108 HOH HOH . P 4 HOH D 20 6109 6109 HOH HOH . P 4 HOH D 21 6111 6111 HOH HOH . P 4 HOH D 22 6112 6112 HOH HOH . P 4 HOH D 23 6113 6113 HOH HOH . P 4 HOH D 24 6127 6127 HOH HOH . P 4 HOH D 25 6130 6130 HOH HOH . P 4 HOH D 26 6132 6132 HOH HOH . P 4 HOH D 27 6155 6155 HOH HOH . P 4 HOH D 28 6162 6162 HOH HOH . P 4 HOH D 29 6163 6163 HOH HOH . P 4 HOH D 30 6182 6182 HOH HOH . P 4 HOH D 31 6216 6216 HOH HOH . P 4 HOH D 32 6217 6217 HOH HOH . P 4 HOH D 33 6218 6218 HOH HOH . P 4 HOH D 34 6219 6219 HOH HOH . P 4 HOH D 35 6220 6220 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 N N6 3L1 . . . J 3 79.292 11.148 20.699 1 32.18 ? N6 3L1 3401 C 1 HETATM 2 C C6 3L1 . . . J 3 80.479 10.671 20.787 1 36.43 ? C6 3L1 3401 C 1 HETATM 3 N N1 3L1 . . . J 3 81.6 11.373 20.791 1 37.23 ? N1 3L1 3401 C 1 HETATM 4 C C2 3L1 . . . J 3 82.94 10.913 20.879 1 36.4 ? C2 3L1 3401 C 1 HETATM 5 N N3 3L1 . . . J 3 83.075 9.489 20.895 1 36.53 ? N3 3L1 3401 C 1 HETATM 6 C C4 3L1 . . . J 3 81.959 8.711 20.773 1 36.73 ? C4 3L1 3401 C 1 HETATM 7 C C5 3L1 . . . J 3 80.692 9.22 20.772 1 36.15 ? C5 3L1 3401 C 1 HETATM 8 N N7 3L1 . . . J 3 79.839 8.182 20.711 1 34.98 ? N7 3L1 3401 C 1 HETATM 9 C C8 3L1 . . . J 3 80.619 7.06 20.739 1 35.81 ? C8 3L1 3401 C 1 HETATM 10 N N9 3L1 . . . J 3 81.949 7.396 20.804 1 37.62 ? N9 3L1 3401 C 1 HETATM 11 C C1' 3L1 . . . J 3 83.048 6.436 20.753 1 39.07 ? C1' 3L1 3401 C 1 HETATM 12 O O4' 3L1 . . . J 3 82.946 5.669 21.985 1 40.71 ? O4' 3L1 3401 C 1 HETATM 13 C C2' 3L1 . . . J 3 83.053 5.485 19.576 1 38.43 ? C2' 3L1 3401 C 1 HETATM 14 C C3' 3L1 . . . J 3 83.657 4.248 20.23 1 39.77 ? C3' 3L1 3401 C 1 HETATM 15 O O3' 3L1 . . . J 3 85.064 4.376 20.468 1 38.38 ? O3' 3L1 3401 C 1 HETATM 16 C C4' 3L1 . . . J 3 82.96 4.262 21.617 1 41.84 ? C4' 3L1 3401 C 1 HETATM 17 C C5' 3L1 . . . J 3 81.54 3.738 21.559 1 42.79 ? C5' 3L1 3401 C 1 HETATM 18 O O5' 3L1 . . . J 3 81.45 2.308 21.413 1 46.71 ? O5' 3L1 3401 C 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 18 #