data_2ZI5 # _model_server_result.job_id Tj763WxmkF3Lkg4rCNkhkg _model_server_result.datetime_utc '2024-12-11 19:44:52' _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":"K","auth_seq_id":4301}' # _entry.id 2ZI5 # _exptl.entry_id 2ZI5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _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 ? 2 E N N ? 2 G N N ? 2 I N N ? 2 K N N # _chem_comp.formula 'C9 H14 N2 O12 P2' _chem_comp.formula_weight 404.161 _chem_comp.id UDP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-DIPHOSPHATE" _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 N1 C2 UDP sing 391 n n N1 C6 UDP sing 392 n n N1 C1' UDP sing 393 n n C2 N3 UDP sing 394 n n C2 O2 UDP doub 395 n n N3 C4 UDP sing 396 n n N3 HN3 UDP sing 397 n n C4 C5 UDP sing 398 n n C4 O4 UDP doub 399 n n C5 C6 UDP doub 400 n n C5 H5 UDP sing 401 n n C6 H6 UDP sing 402 n n C1' C2' UDP sing 403 n n C1' O4' UDP sing 404 n n C1' H1' UDP sing 405 n n C2' O2' UDP sing 406 n n C2' C3' UDP sing 407 n n C2' H2' UDP sing 408 n n O2' HO2' UDP sing 409 n n C3' C4' UDP sing 410 n n C3' O3' UDP sing 411 n n C3' H3' UDP sing 412 n n C4' O4' UDP sing 413 n n C4' C5' UDP sing 414 n n C4' H4' UDP sing 415 n n O3' HO3' UDP sing 416 n n C5' O5' UDP sing 417 n n C5' "H5'1" UDP sing 418 n n C5' "H5'2" UDP sing 419 n n O5' PA UDP sing 420 n n PA O1A UDP doub 421 n n PA O2A UDP sing 422 n n PA O3A UDP sing 423 n n O2A HOA2 UDP sing 424 n n O3A PB UDP sing 425 n n PB O1B UDP doub 426 n n PB O2B UDP sing 427 n n PB O3B UDP sing 428 n n O2B HOB2 UDP sing 429 n n O3B HOB3 UDP sing 430 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 N1 UDP . . . K 2 99.305 60.098 -14.885 1 32.11 ? N1 UDP 4301 D 1 HETATM 2 C C2 UDP . . . K 2 100.342 60.276 -13.97 1 33.67 ? C2 UDP 4301 D 1 HETATM 3 N N3 UDP . . . K 2 100.329 59.63 -12.762 1 34.38 ? N3 UDP 4301 D 1 HETATM 4 C C4 UDP . . . K 2 99.313 58.733 -12.522 1 34.88 ? C4 UDP 4301 D 1 HETATM 5 C C5 UDP . . . K 2 98.23 58.593 -13.392 1 32.48 ? C5 UDP 4301 D 1 HETATM 6 C C6 UDP . . . K 2 98.268 59.259 -14.602 1 32.11 ? C6 UDP 4301 D 1 HETATM 7 O O2 UDP . . . K 2 101.276 61.012 -14.204 1 34.28 ? O2 UDP 4301 D 1 HETATM 8 O O4 UDP . . . K 2 99.225 58.205 -11.414 1 42.96 ? O4 UDP 4301 D 1 HETATM 9 C C1' UDP . . . K 2 99.051 61.098 -15.925 1 31.4 ? C1' UDP 4301 D 1 HETATM 10 C C2' UDP . . . K 2 98.908 60.503 -17.298 1 31.81 ? C2' UDP 4301 D 1 HETATM 11 O O2' UDP . . . K 2 100.134 60.346 -17.935 1 34.41 ? O2' UDP 4301 D 1 HETATM 12 C C3' UDP . . . K 2 98.081 61.542 -18.027 1 31.64 ? C3' UDP 4301 D 1 HETATM 13 C C4' UDP . . . K 2 97.225 62.109 -16.916 1 31.48 ? C4' UDP 4301 D 1 HETATM 14 O O4' UDP . . . K 2 97.796 61.72 -15.671 1 32.24 ? O4' UDP 4301 D 1 HETATM 15 O O3' UDP . . . K 2 98.939 62.568 -18.427 1 28.65 ? O3' UDP 4301 D 1 HETATM 16 C C5' UDP . . . K 2 95.779 61.614 -17.061 1 31.11 ? C5' UDP 4301 D 1 HETATM 17 O O5' UDP . . . K 2 95.753 60.183 -16.738 1 31.73 ? O5' UDP 4301 D 1 HETATM 18 P PA UDP . . . K 2 94.832 59.273 -17.676 1 31.76 ? PA UDP 4301 D 1 HETATM 19 O O1A UDP . . . K 2 94.593 59.718 -19.061 1 22.68 ? O1A UDP 4301 D 1 HETATM 20 O O2A UDP . . . K 2 95.236 57.886 -17.591 1 30.7 ? O2A UDP 4301 D 1 HETATM 21 O O3A UDP . . . K 2 93.42 59.453 -16.868 1 31.76 ? O3A UDP 4301 D 1 HETATM 22 P PB UDP . . . K 2 91.929 58.985 -17.363 1 29.82 ? PB UDP 4301 D 1 HETATM 23 O O1B UDP . . . K 2 92.133 57.943 -18.38 1 27.92 ? O1B UDP 4301 D 1 HETATM 24 O O2B UDP . . . K 2 91.213 60.158 -17.935 1 36.07 ? O2B UDP 4301 D 1 HETATM 25 O O3B UDP . . . K 2 91.204 58.706 -16.137 1 29.35 ? O3B UDP 4301 D 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 25 #