data_1VD3 # _model_server_result.job_id cZysOyXMAP0KE1RFg9kUHA _model_server_result.datetime_utc '2024-11-14 23:29:49' _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 1vd3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":214}' # _entry.id 1VD3 # _exptl.entry_id 1VD3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 324.181 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHORIC ACID MONO-[2-(2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-4-HYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-YL] ESTER' _entity.pdbx_number_of_molecules 1 _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 1VD3 _cell.length_a 37.232 _cell.length_b 68.984 _cell.length_c 73.863 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VD3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 22 A CYS 18 1_555 A SG CYS 28 A CYS 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf2 A SG CYS 29 A CYS 25 1_555 A SG CYS 85 A CYS 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf3 A SG CYS 58 A CYS 54 1_555 A SG CYS 104 A CYS 100 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf4 A SG CYS 163 A CYS 159 1_555 A SG CYS 199 A CYS 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 A SG CYS 179 A CYS 175 1_555 A SG CYS 190 A CYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? # _chem_comp.formula 'C9 H13 N2 O9 P' _chem_comp.formula_weight 324.181 _chem_comp.id U2P _chem_comp.mon_nstd_flag n _chem_comp.name 'PHOSPHORIC ACID MONO-[2-(2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-4-HYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-YL] ESTER' _chem_comp.type 'rna linking' _chem_comp.pdbx_synonyms "URIDINE-2'-PHOSPHATE;2'-URIDINEMONOPHOSPHATE" # 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' U2P sing 358 n n O5' H5' U2P sing 359 n n C5' C4' U2P sing 360 n n C5' "H5'1" U2P sing 361 n n C5' "H5'2" U2P sing 362 n n C4' O4' U2P sing 363 n n C4' C3' U2P sing 364 n n C4' H4' U2P sing 365 n n O4' C1' U2P sing 366 n n C1' N1 U2P sing 367 n n C1' C2' U2P sing 368 n n C1' H1' U2P sing 369 n n N1 C6 U2P sing 370 n n N1 C2 U2P sing 371 n n C6 C5 U2P doub 372 n n C6 H6 U2P sing 373 n n C5 C4 U2P sing 374 n n C5 H5 U2P sing 375 n n C4 O4 U2P doub 376 n n C4 N3 U2P sing 377 n n N3 C2 U2P sing 378 n n N3 HN3 U2P sing 379 n n C2 O2 U2P doub 380 n n C2' O2' U2P sing 381 n n C2' C3' U2P sing 382 n n C2' H2' U2P sing 383 n n O2' P U2P sing 384 n n P O1P U2P doub 385 n n P O2P U2P sing 386 n n P O3P U2P sing 387 n n O2P H2P U2P sing 388 n n O3P H3P U2P sing 389 n n C3' O3' U2P sing 390 n n C3' H3' U2P sing 391 n n O3' H1 U2P sing 392 n n # _atom_sites.entry_id 1VD3 _atom_sites.fract_transf_matrix[1][1] 0.026859 _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] 0.014496 _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] 0.013539 _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 B 2 U2P A 1 214 0 U2P U2P . C 3 HOH A 1 215 1 HOH HOH . C 3 HOH A 2 216 2 HOH HOH . C 3 HOH A 3 217 3 HOH HOH . C 3 HOH A 4 218 4 HOH HOH . C 3 HOH A 5 219 5 HOH HOH . C 3 HOH A 6 220 6 HOH HOH . C 3 HOH A 7 221 7 HOH HOH . C 3 HOH A 8 222 8 HOH HOH . C 3 HOH A 9 223 9 HOH HOH . C 3 HOH A 10 224 10 HOH HOH . C 3 HOH A 11 225 11 HOH HOH . C 3 HOH A 12 226 12 HOH HOH . C 3 HOH A 13 227 13 HOH HOH . C 3 HOH A 14 228 14 HOH HOH . C 3 HOH A 15 229 15 HOH HOH . C 3 HOH A 16 230 16 HOH HOH . C 3 HOH A 17 231 17 HOH HOH . C 3 HOH A 18 232 18 HOH HOH . C 3 HOH A 19 233 19 HOH HOH . C 3 HOH A 20 234 20 HOH HOH . C 3 HOH A 21 235 21 HOH HOH . C 3 HOH A 22 236 22 HOH HOH . C 3 HOH A 23 237 23 HOH HOH . C 3 HOH A 24 238 24 HOH HOH . C 3 HOH A 25 239 25 HOH HOH . C 3 HOH A 26 240 26 HOH HOH . C 3 HOH A 27 241 27 HOH HOH . C 3 HOH A 28 242 28 HOH HOH . C 3 HOH A 29 243 29 HOH HOH . C 3 HOH A 30 244 30 HOH HOH . C 3 HOH A 31 245 31 HOH HOH . C 3 HOH A 32 246 32 HOH HOH . C 3 HOH A 33 247 33 HOH HOH . C 3 HOH A 34 248 34 HOH HOH . C 3 HOH A 35 249 35 HOH HOH . C 3 HOH A 36 250 36 HOH HOH . C 3 HOH A 37 251 37 HOH HOH . C 3 HOH A 38 252 38 HOH HOH . C 3 HOH A 39 253 39 HOH HOH . C 3 HOH A 40 254 40 HOH HOH . C 3 HOH A 41 255 41 HOH HOH . C 3 HOH A 42 256 42 HOH HOH . C 3 HOH A 43 257 43 HOH HOH . C 3 HOH A 44 258 44 HOH HOH . C 3 HOH A 45 259 45 HOH HOH . C 3 HOH A 46 260 46 HOH HOH . C 3 HOH A 47 261 47 HOH HOH . C 3 HOH A 48 262 48 HOH HOH . C 3 HOH A 49 263 49 HOH HOH . C 3 HOH A 50 264 50 HOH HOH . C 3 HOH A 51 265 51 HOH HOH . C 3 HOH A 52 266 52 HOH HOH . C 3 HOH A 53 267 53 HOH HOH . C 3 HOH A 54 268 54 HOH HOH . C 3 HOH A 55 269 55 HOH HOH . C 3 HOH A 56 270 56 HOH HOH . C 3 HOH A 57 271 57 HOH HOH . C 3 HOH A 58 272 58 HOH HOH . C 3 HOH A 59 273 59 HOH HOH . C 3 HOH A 60 274 60 HOH HOH . C 3 HOH A 61 275 61 HOH HOH . C 3 HOH A 62 276 62 HOH HOH . C 3 HOH A 63 277 63 HOH HOH . C 3 HOH A 64 278 64 HOH HOH . C 3 HOH A 65 279 65 HOH HOH . C 3 HOH A 66 280 66 HOH HOH . C 3 HOH A 67 281 67 HOH HOH . C 3 HOH A 68 282 68 HOH HOH . C 3 HOH A 69 283 69 HOH HOH . C 3 HOH A 70 284 70 HOH HOH . C 3 HOH A 71 285 71 HOH HOH . C 3 HOH A 72 286 72 HOH HOH . C 3 HOH A 73 287 73 HOH HOH . C 3 HOH A 74 288 74 HOH HOH . C 3 HOH A 75 289 75 HOH HOH . C 3 HOH A 76 290 76 HOH HOH . C 3 HOH A 77 291 77 HOH HOH . C 3 HOH A 78 292 78 HOH HOH . C 3 HOH A 79 293 79 HOH HOH . C 3 HOH A 80 294 80 HOH HOH . C 3 HOH A 81 295 81 HOH HOH . C 3 HOH A 82 296 82 HOH HOH . C 3 HOH A 83 297 83 HOH HOH . C 3 HOH A 84 298 84 HOH HOH . C 3 HOH A 85 299 85 HOH HOH . C 3 HOH A 86 300 86 HOH HOH . C 3 HOH A 87 301 87 HOH HOH . C 3 HOH A 88 302 88 HOH HOH . C 3 HOH A 89 303 89 HOH HOH . C 3 HOH A 90 304 90 HOH HOH . C 3 HOH A 91 305 91 HOH HOH . C 3 HOH A 92 306 92 HOH HOH . C 3 HOH A 93 307 93 HOH HOH . C 3 HOH A 94 308 94 HOH HOH . C 3 HOH A 95 309 95 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 O O5' U2P . . . B 2 -28.446 34.223 -60.549 1 47.66 ? O5' U2P 214 A 1 HETATM 2 C C5' U2P . . . B 2 -27.828 33.821 -59.302 1 37.5 ? C5' U2P 214 A 1 HETATM 3 C C4' U2P . . . B 2 -27.278 32.393 -59.426 1 34.84 ? C4' U2P 214 A 1 HETATM 4 O O4' U2P . . . B 2 -26.665 31.982 -58.114 1 32.96 ? O4' U2P 214 A 1 HETATM 5 C C1' U2P . . . B 2 -27.27 30.758 -57.447 1 31.77 ? C1' U2P 214 A 1 HETATM 6 N N1 U2P . . . B 2 -27.959 30.981 -56.102 1 28.14 ? N1 U2P 214 A 1 HETATM 7 C C6 U2P . . . B 2 -28.661 32.159 -56.02 1 24.92 ? C6 U2P 214 A 1 HETATM 8 C C5 U2P . . . B 2 -29.557 32.435 -54.954 1 27 ? C5 U2P 214 A 1 HETATM 9 C C4 U2P . . . B 2 -29.691 31.426 -53.879 1 24.74 ? C4 U2P 214 A 1 HETATM 10 O O4 U2P . . . B 2 -30.514 31.536 -52.976 1 24.13 ? O4 U2P 214 A 1 HETATM 11 N N3 U2P . . . B 2 -28.801 30.309 -53.963 1 23.63 ? N3 U2P 214 A 1 HETATM 12 C C2 U2P . . . B 2 -27.901 30.036 -55.021 1 23.96 ? C2 U2P 214 A 1 HETATM 13 O O2 U2P . . . B 2 -27.167 29.071 -54.967 1 28.27 ? O2 U2P 214 A 1 HETATM 14 C C2' U2P . . . B 2 -27.998 30.135 -58.658 1 32.5 ? C2' U2P 214 A 1 HETATM 15 O O2' U2P . . . B 2 -27.114 29.316 -59.481 1 32.98 ? O2' U2P 214 A 1 HETATM 16 P P U2P . . . B 2 -26.636 27.845 -59.194 1 21.39 ? P U2P 214 A 1 HETATM 17 O O1P U2P . . . B 2 -25.638 27.027 -59.835 1 27.21 ? O1P U2P 214 A 1 HETATM 18 O O2P U2P . . . B 2 -26.734 27.583 -57.725 1 29.26 ? O2P U2P 214 A 1 HETATM 19 O O3P U2P . . . B 2 -27.774 27.105 -59.711 1 25.63 ? O3P U2P 214 A 1 HETATM 20 C C3' U2P . . . B 2 -28.408 31.339 -59.523 1 32.12 ? C3' U2P 214 A 1 HETATM 21 O O3' U2P . . . B 2 -28.553 30.876 -60.916 1 31.16 ? O3' U2P 214 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 368 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 21 #