data_4O8R # _model_server_result.job_id OfCREtrtNT4jx2boavRAyw _model_server_result.datetime_utc '2024-11-07 16:45:51' _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 4o8r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":301}' # _entry.id 4O8R # _exptl.entry_id 4O8R _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 326.197 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 12 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 91.59 _cell.angle_gamma 90 _cell.entry_id 4O8R _cell.length_a 147.899 _cell.length_b 101.8 _cell.length_c 192.845 _cell.Z_PDB 52 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4O8R _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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 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 PISA dimeric 2 author_and_software_defined_assembly 4 PISA dimeric 2 author_and_software_defined_assembly 5 PISA dimeric 2 author_and_software_defined_assembly 6 PISA dimeric 2 author_and_software_defined_assembly 7 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,N,O,P,AA,BA 1 1 C,D,Q,R,CA,DA 2 1 E,F,S,T,EA,FA 3 1 G,H,U,V,GA,HA 4 1 I,J,W,IA,JA 5 1 K,L,X,Y,KA 6 1 M,Z,LA 7 1,2 # 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' 2_455 -x-1,y,-z -1 0 0 0 1 0 0 0 -1 -147.899 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 N N N ? 2 P N N ? 2 Q N N ? 2 R N N ? 2 S N N ? 2 T N N ? 2 U N N ? 2 V N N ? 2 W N N ? 2 X N N ? 2 Y N N ? 2 Z N N # _chem_comp.formula 'C9 H15 N2 O9 P' _chem_comp.formula_weight 326.197 _chem_comp.id H2U _chem_comp.mon_nstd_flag n _chem_comp.name "5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE" _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 P OP1 H2U doub 129 n n P OP2 H2U sing 130 n n P OP3 H2U sing 131 n n P O5' H2U sing 132 n n OP2 HOP2 H2U sing 133 n n OP3 HOP3 H2U sing 134 n n O5' C5' H2U sing 135 n n C5' C4' H2U sing 136 n n C5' H5' H2U sing 137 n n C5' "H5''" H2U sing 138 n n C4' O4' H2U sing 139 n n C4' C3' H2U sing 140 n n C4' H4' H2U sing 141 n n O4' C1' H2U sing 142 n n C3' O3' H2U sing 143 n n C3' C2' H2U sing 144 n n C3' H3' H2U sing 145 n n O3' HO3' H2U sing 146 n n C1' C2' H2U sing 147 n n C1' N1 H2U sing 148 n n C1' H1' H2U sing 149 n n C2' O2' H2U sing 150 n n C2' H2' H2U sing 151 n n O2' HO2' H2U sing 152 n n N1 C2 H2U sing 153 n n N1 C6 H2U sing 154 n n C2 O2 H2U doub 155 n n C2 N3 H2U sing 156 n n N3 C4 H2U sing 157 n n N3 HN3 H2U sing 158 n n C4 O4 H2U doub 159 n n C4 C5 H2U sing 160 n n C5 C6 H2U sing 161 n n C5 H51 H2U sing 162 n n C5 H52 H2U sing 163 n n C6 H61 H2U sing 164 n n C6 H62 H2U sing 165 n n # _atom_sites.entry_id 4O8R _atom_sites.fract_transf_matrix[1][1] 0.006761 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000188 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009823 _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] 0.005188 _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 N 2 H2U A 1 301 229 H2U H2U . O 3 CL A 1 302 1 CL CL . P 2 H2U B 1 301 229 H2U H2U . Q 2 H2U C 1 301 229 H2U H2U . R 2 H2U D 1 301 229 H2U H2U . S 2 H2U E 1 301 229 H2U H2U . T 2 H2U F 1 301 229 H2U H2U . U 2 H2U G 1 301 229 H2U H2U . V 2 H2U H 1 301 229 H2U H2U . W 2 H2U J 1 301 229 H2U H2U . X 2 H2U K 1 301 229 H2U H2U . Y 2 H2U L 1 301 229 H2U H2U . Z 2 H2U M 1 301 229 H2U H2U . AA 4 HOH A 1 401 1 HOH HOH . AA 4 HOH A 2 402 3 HOH HOH . AA 4 HOH A 3 403 8 HOH HOH . AA 4 HOH A 4 404 9 HOH HOH . AA 4 HOH A 5 405 12 HOH HOH . AA 4 HOH A 6 406 13 HOH HOH . AA 4 HOH A 7 407 14 HOH HOH . AA 4 HOH A 8 408 17 HOH HOH . AA 4 HOH A 9 409 18 HOH HOH . AA 4 HOH A 10 410 23 HOH HOH . AA 4 HOH A 11 411 24 HOH HOH . AA 4 HOH A 12 412 26 HOH HOH . AA 4 HOH A 13 413 32 HOH HOH . AA 4 HOH A 14 414 39 HOH HOH . AA 4 HOH A 15 415 42 HOH HOH . AA 4 HOH A 16 416 47 HOH HOH . AA 4 HOH A 17 417 49 HOH HOH . AA 4 HOH A 18 418 56 HOH HOH . AA 4 HOH A 19 419 59 HOH HOH . AA 4 HOH A 20 420 60 HOH HOH . AA 4 HOH A 21 421 72 HOH HOH . AA 4 HOH A 22 422 73 HOH HOH . AA 4 HOH A 23 423 74 HOH HOH . AA 4 HOH A 24 424 80 HOH HOH . AA 4 HOH A 25 425 81 HOH HOH . AA 4 HOH A 26 426 84 HOH HOH . AA 4 HOH A 27 427 111 HOH HOH . AA 4 HOH A 28 428 114 HOH HOH . AA 4 HOH A 29 429 133 HOH HOH . AA 4 HOH A 30 430 148 HOH HOH . AA 4 HOH A 31 431 158 HOH HOH . AA 4 HOH A 32 432 191 HOH HOH . AA 4 HOH A 33 433 195 HOH HOH . AA 4 HOH A 34 434 196 HOH HOH . AA 4 HOH A 35 435 197 HOH HOH . AA 4 HOH A 36 436 199 HOH HOH . BA 4 HOH B 1 401 10 HOH HOH . BA 4 HOH B 2 402 11 HOH HOH . BA 4 HOH B 3 403 15 HOH HOH . BA 4 HOH B 4 404 25 HOH HOH . BA 4 HOH B 5 405 30 HOH HOH . BA 4 HOH B 6 406 37 HOH HOH . BA 4 HOH B 7 407 61 HOH HOH . BA 4 HOH B 8 408 75 HOH HOH . BA 4 HOH B 9 409 86 HOH HOH . BA 4 HOH B 10 410 88 HOH HOH . BA 4 HOH B 11 411 104 HOH HOH . BA 4 HOH B 12 412 112 HOH HOH . BA 4 HOH B 13 413 120 HOH HOH . BA 4 HOH B 14 414 135 HOH HOH . BA 4 HOH B 15 415 144 HOH HOH . BA 4 HOH B 16 416 147 HOH HOH . BA 4 HOH B 17 417 156 HOH HOH . BA 4 HOH B 18 418 162 HOH HOH . BA 4 HOH B 19 419 163 HOH HOH . BA 4 HOH B 20 420 165 HOH HOH . BA 4 HOH B 21 421 166 HOH HOH . BA 4 HOH B 22 422 190 HOH HOH . CA 4 HOH C 1 401 4 HOH HOH . CA 4 HOH C 2 402 19 HOH HOH . CA 4 HOH C 3 403 29 HOH HOH . CA 4 HOH C 4 404 31 HOH HOH . CA 4 HOH C 5 405 34 HOH HOH . CA 4 HOH C 6 406 38 HOH HOH . CA 4 HOH C 7 407 40 HOH HOH . CA 4 HOH C 8 408 43 HOH HOH . CA 4 HOH C 9 409 44 HOH HOH . CA 4 HOH C 10 410 48 HOH HOH . CA 4 HOH C 11 411 50 HOH HOH . CA 4 HOH C 12 412 51 HOH HOH . CA 4 HOH C 13 413 53 HOH HOH . CA 4 HOH C 14 414 62 HOH HOH . CA 4 HOH C 15 415 67 HOH HOH . CA 4 HOH C 16 416 78 HOH HOH . CA 4 HOH C 17 417 79 HOH HOH . CA 4 HOH C 18 418 85 HOH HOH . CA 4 HOH C 19 419 96 HOH HOH . CA 4 HOH C 20 420 100 HOH HOH . CA 4 HOH C 21 421 101 HOH HOH . CA 4 HOH C 22 422 102 HOH HOH . CA 4 HOH C 23 423 105 HOH HOH . CA 4 HOH C 24 424 108 HOH HOH . CA 4 HOH C 25 425 117 HOH HOH . CA 4 HOH C 26 426 121 HOH HOH . CA 4 HOH C 27 427 122 HOH HOH . CA 4 HOH C 28 428 123 HOH HOH . CA 4 HOH C 29 429 126 HOH HOH . CA 4 HOH C 30 430 140 HOH HOH . CA 4 HOH C 31 431 143 HOH HOH . CA 4 HOH C 32 432 149 HOH HOH . CA 4 HOH C 33 433 150 HOH HOH . CA 4 HOH C 34 434 167 HOH HOH . DA 4 HOH D 1 401 2 HOH HOH . DA 4 HOH D 2 402 5 HOH HOH . DA 4 HOH D 3 403 6 HOH HOH . DA 4 HOH D 4 404 33 HOH HOH . DA 4 HOH D 5 405 52 HOH HOH . DA 4 HOH D 6 406 77 HOH HOH . DA 4 HOH D 7 407 90 HOH HOH . DA 4 HOH D 8 408 94 HOH HOH . DA 4 HOH D 9 409 98 HOH HOH . DA 4 HOH D 10 410 103 HOH HOH . DA 4 HOH D 11 411 110 HOH HOH . DA 4 HOH D 12 412 115 HOH HOH . DA 4 HOH D 13 413 116 HOH HOH . DA 4 HOH D 14 414 127 HOH HOH . DA 4 HOH D 15 415 132 HOH HOH . DA 4 HOH D 16 416 153 HOH HOH . DA 4 HOH D 17 417 160 HOH HOH . DA 4 HOH D 18 418 168 HOH HOH . DA 4 HOH D 19 419 194 HOH HOH . EA 4 HOH E 1 401 93 HOH HOH . EA 4 HOH E 2 402 134 HOH HOH . EA 4 HOH E 3 403 159 HOH HOH . EA 4 HOH E 4 404 169 HOH HOH . EA 4 HOH E 5 405 170 HOH HOH . EA 4 HOH E 6 406 171 HOH HOH . EA 4 HOH E 7 407 172 HOH HOH . FA 4 HOH F 1 401 20 HOH HOH . FA 4 HOH F 2 402 28 HOH HOH . FA 4 HOH F 3 403 113 HOH HOH . FA 4 HOH F 4 404 119 HOH HOH . FA 4 HOH F 5 405 124 HOH HOH . FA 4 HOH F 6 406 130 HOH HOH . FA 4 HOH F 7 407 141 HOH HOH . FA 4 HOH F 8 408 146 HOH HOH . FA 4 HOH F 9 409 173 HOH HOH . FA 4 HOH F 10 410 174 HOH HOH . FA 4 HOH F 11 411 186 HOH HOH . GA 4 HOH G 1 401 118 HOH HOH . GA 4 HOH G 2 402 138 HOH HOH . GA 4 HOH G 3 403 175 HOH HOH . GA 4 HOH G 4 404 176 HOH HOH . GA 4 HOH G 5 405 177 HOH HOH . GA 4 HOH G 6 406 193 HOH HOH . HA 4 HOH H 1 401 54 HOH HOH . HA 4 HOH H 2 402 137 HOH HOH . HA 4 HOH H 3 403 161 HOH HOH . HA 4 HOH H 4 404 178 HOH HOH . HA 4 HOH H 5 405 179 HOH HOH . HA 4 HOH H 6 406 187 HOH HOH . IA 4 HOH I 1 301 22 HOH HOH . IA 4 HOH I 2 302 45 HOH HOH . IA 4 HOH I 3 303 46 HOH HOH . IA 4 HOH I 4 304 58 HOH HOH . IA 4 HOH I 5 305 82 HOH HOH . IA 4 HOH I 6 306 83 HOH HOH . IA 4 HOH I 7 307 106 HOH HOH . IA 4 HOH I 8 308 107 HOH HOH . IA 4 HOH I 9 309 109 HOH HOH . IA 4 HOH I 10 310 192 HOH HOH . IA 4 HOH I 11 311 198 HOH HOH . JA 4 HOH J 1 401 27 HOH HOH . JA 4 HOH J 2 402 36 HOH HOH . JA 4 HOH J 3 403 55 HOH HOH . JA 4 HOH J 4 404 63 HOH HOH . JA 4 HOH J 5 405 64 HOH HOH . JA 4 HOH J 6 406 66 HOH HOH . JA 4 HOH J 7 407 69 HOH HOH . JA 4 HOH J 8 408 87 HOH HOH . JA 4 HOH J 9 409 91 HOH HOH . JA 4 HOH J 10 410 92 HOH HOH . JA 4 HOH J 11 411 95 HOH HOH . JA 4 HOH J 12 412 99 HOH HOH . JA 4 HOH J 13 413 131 HOH HOH . JA 4 HOH J 14 414 139 HOH HOH . JA 4 HOH J 15 415 142 HOH HOH . JA 4 HOH J 16 416 152 HOH HOH . JA 4 HOH J 17 417 154 HOH HOH . JA 4 HOH J 18 418 164 HOH HOH . JA 4 HOH J 19 419 180 HOH HOH . JA 4 HOH J 20 420 181 HOH HOH . KA 4 HOH K 1 401 157 HOH HOH . KA 4 HOH K 2 402 182 HOH HOH . KA 4 HOH K 3 403 183 HOH HOH . KA 4 HOH K 4 404 188 HOH HOH . LA 4 HOH M 1 401 7 HOH HOH . LA 4 HOH M 2 402 16 HOH HOH . LA 4 HOH M 3 403 21 HOH HOH . LA 4 HOH M 4 404 35 HOH HOH . LA 4 HOH M 5 405 41 HOH HOH . LA 4 HOH M 6 406 57 HOH HOH . LA 4 HOH M 7 407 65 HOH HOH . LA 4 HOH M 8 408 68 HOH HOH . LA 4 HOH M 9 409 70 HOH HOH . LA 4 HOH M 10 410 71 HOH HOH . LA 4 HOH M 11 411 76 HOH HOH . LA 4 HOH M 12 412 89 HOH HOH . LA 4 HOH M 13 413 97 HOH HOH . LA 4 HOH M 14 414 125 HOH HOH . LA 4 HOH M 15 415 128 HOH HOH . LA 4 HOH M 16 416 129 HOH HOH . LA 4 HOH M 17 417 136 HOH HOH . LA 4 HOH M 18 418 145 HOH HOH . LA 4 HOH M 19 419 151 HOH HOH . LA 4 HOH M 20 420 155 HOH HOH . LA 4 HOH M 21 421 184 HOH HOH . LA 4 HOH M 22 422 185 HOH HOH . LA 4 HOH M 23 423 189 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 P H2U . . . T 2 -63.386 42.405 -55.869 1 84.51 ? P H2U 301 F 1 HETATM 2 O OP1 H2U . . . T 2 -63.627 41.642 -57.175 1 85.95 ? OP1 H2U 301 F 1 HETATM 3 O OP2 H2U . . . T 2 -64.582 42.928 -55.083 1 87.56 ? OP2 H2U 301 F 1 HETATM 4 O OP3 H2U . . . T 2 -62.591 41.49 -54.938 1 84.92 ? OP3 H2U 301 F 1 HETATM 5 O O5' H2U . . . T 2 -62.492 43.68 -56.209 1 82.97 ? O5' H2U 301 F 1 HETATM 6 C C5' H2U . . . T 2 -61.176 43.54 -56.733 1 79.46 ? C5' H2U 301 F 1 HETATM 7 C C4' H2U . . . T 2 -60.513 44.883 -56.923 1 75.66 ? C4' H2U 301 F 1 HETATM 8 O O4' H2U . . . T 2 -59.371 44.733 -57.812 1 73.18 ? O4' H2U 301 F 1 HETATM 9 C C3' H2U . . . T 2 -61.394 45.961 -57.55 1 75.64 ? C3' H2U 301 F 1 HETATM 10 O O3' H2U . . . T 2 -60.996 47.239 -57.052 1 72.68 ? O3' H2U 301 F 1 HETATM 11 C C1' H2U . . . T 2 -59.534 45.573 -58.941 1 71.99 ? C1' H2U 301 F 1 HETATM 12 C C2' H2U . . . T 2 -61.031 45.856 -59.027 1 74.67 ? C2' H2U 301 F 1 HETATM 13 O O2' H2U . . . T 2 -61.311 47.012 -59.789 1 73.32 ? O2' H2U 301 F 1 HETATM 14 N N1 H2U . . . T 2 -58.967 44.889 -60.114 1 71.81 ? N1 H2U 301 F 1 HETATM 15 C C2 H2U . . . T 2 -59.403 43.663 -60.474 1 74.54 ? C2 H2U 301 F 1 HETATM 16 O O2 H2U . . . T 2 -60.285 43.133 -59.816 1 77.34 ? O2 H2U 301 F 1 HETATM 17 N N3 H2U . . . T 2 -58.899 43.011 -61.535 1 74.67 ? N3 H2U 301 F 1 HETATM 18 C C4 H2U . . . T 2 -57.922 43.551 -62.289 1 72.36 ? C4 H2U 301 F 1 HETATM 19 O O4 H2U . . . T 2 -57.495 42.936 -63.239 1 72.86 ? O4 H2U 301 F 1 HETATM 20 C C5 H2U . . . T 2 -57.124 44.702 -61.732 1 69.55 ? C5 H2U 301 F 1 HETATM 21 C C6 H2U . . . T 2 -58.076 45.647 -60.996 1 69.4 ? C6 H2U 301 F 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 38 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 21 #