data_7BIX # _model_server_result.job_id HxffaXeNMPaNqfkRggNEBg _model_server_result.datetime_utc '2024-11-21 18:27:05' _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 7bix # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":300}' # _entry.id 7BIX # _exptl.entry_id 7BIX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 3 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 8 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 121.39 _cell.angle_gamma 90 _cell.entry_id 7BIX _cell.length_a 197.47 _cell.length_b 152.82 _cell.length_c 125.11 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7BIX _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 hexameric 6 author_and_software_defined_assembly 1 PISA hexameric 6 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,M,N,O,P,Q,R,S,AA,BA,CA,DA,EA,FA 1 1 G,H,I,J,K,L,T,U,V,W,X,Y,Z,GA,HA,IA,JA,KA,LA 2 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 N N N ? 3 P N N ? 3 R N N ? 3 S N N ? 3 U N N ? 3 W N N ? 3 Y N N ? 3 Z 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 330 n n N1 C6 UDP sing 331 n n N1 C1' UDP sing 332 n n C2 N3 UDP sing 333 n n C2 O2 UDP doub 334 n n N3 C4 UDP sing 335 n n N3 HN3 UDP sing 336 n n C4 C5 UDP sing 337 n n C4 O4 UDP doub 338 n n C5 C6 UDP doub 339 n n C5 H5 UDP sing 340 n n C6 H6 UDP sing 341 n n C1' C2' UDP sing 342 n n C1' O4' UDP sing 343 n n C1' H1' UDP sing 344 n n C2' O2' UDP sing 345 n n C2' C3' UDP sing 346 n n C2' H2' UDP sing 347 n n O2' HO2' UDP sing 348 n n C3' C4' UDP sing 349 n n C3' O3' UDP sing 350 n n C3' H3' UDP sing 351 n n C4' O4' UDP sing 352 n n C4' C5' UDP sing 353 n n C4' H4' UDP sing 354 n n O3' HO3' UDP sing 355 n n C5' O5' UDP sing 356 n n C5' "H5'1" UDP sing 357 n n C5' "H5'2" UDP sing 358 n n O5' PA UDP sing 359 n n PA O1A UDP doub 360 n n PA O2A UDP sing 361 n n PA O3A UDP sing 362 n n O2A HOA2 UDP sing 363 n n O3A PB UDP sing 364 n n PB O1B UDP doub 365 n n PB O2B UDP sing 366 n n PB O3B UDP sing 367 n n O2B HOB2 UDP sing 368 n n O3B HOB3 UDP sing 369 n n # _atom_sites.entry_id 7BIX _atom_sites.fract_transf_matrix[1][1] 0.005064 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00309 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006544 _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] 0.009363 _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 M 2 UTP A 1 301 1 UTP UTP . N 3 UDP B 1 300 300 UDP UDP . O 2 UTP C 1 301 2 UTP UTP . P 3 UDP C 1 302 300 UDP UDP . Q 2 UTP D 1 301 5 UTP UTP . R 3 UDP D 1 302 263 UDP UDP . S 3 UDP E 1 301 263 UDP UDP . T 2 UTP G 1 301 4 UTP UTP . U 3 UDP H 1 301 263 UDP UDP . V 2 UTP I 1 301 3 UTP UTP . W 3 UDP I 1 302 263 UDP UDP . X 2 UTP J 1 301 6 UTP UTP . Y 3 UDP J 1 302 263 UDP UDP . Z 3 UDP K 1 301 263 UDP UDP . AA 4 HOH A 1 401 26 HOH HOH . AA 4 HOH A 2 402 22 HOH HOH . AA 4 HOH A 3 403 21 HOH HOH . BA 4 HOH B 1 401 25 HOH HOH . BA 4 HOH B 2 402 23 HOH HOH . CA 4 HOH C 1 401 31 HOH HOH . CA 4 HOH C 2 402 32 HOH HOH . CA 4 HOH C 3 403 7 HOH HOH . CA 4 HOH C 4 404 34 HOH HOH . DA 4 HOH D 1 401 15 HOH HOH . DA 4 HOH D 2 402 24 HOH HOH . DA 4 HOH D 3 403 38 HOH HOH . DA 4 HOH D 4 404 20 HOH HOH . DA 4 HOH D 5 405 37 HOH HOH . EA 4 HOH E 1 401 6 HOH HOH . EA 4 HOH E 2 402 33 HOH HOH . EA 4 HOH E 3 403 5 HOH HOH . EA 4 HOH E 4 404 36 HOH HOH . EA 4 HOH E 5 405 27 HOH HOH . FA 4 HOH F 1 301 17 HOH HOH . FA 4 HOH F 2 302 19 HOH HOH . FA 4 HOH F 3 303 18 HOH HOH . FA 4 HOH F 4 304 16 HOH HOH . FA 4 HOH F 5 305 28 HOH HOH . FA 4 HOH F 6 306 35 HOH HOH . GA 4 HOH G 1 401 44 HOH HOH . GA 4 HOH G 2 402 2 HOH HOH . GA 4 HOH G 3 403 1 HOH HOH . GA 4 HOH G 4 404 30 HOH HOH . GA 4 HOH G 5 405 3 HOH HOH . GA 4 HOH G 6 406 4 HOH HOH . HA 4 HOH H 1 401 29 HOH HOH . IA 4 HOH I 1 401 46 HOH HOH . IA 4 HOH I 2 402 8 HOH HOH . IA 4 HOH I 3 403 45 HOH HOH . IA 4 HOH I 4 404 39 HOH HOH . IA 4 HOH I 5 405 40 HOH HOH . JA 4 HOH J 1 401 4 HOH HOH . JA 4 HOH J 2 402 13 HOH HOH . JA 4 HOH J 3 403 9 HOH HOH . JA 4 HOH J 4 404 42 HOH HOH . JA 4 HOH J 5 405 43 HOH HOH . JA 4 HOH J 6 406 14 HOH HOH . JA 4 HOH J 7 407 41 HOH HOH . JA 4 HOH J 8 408 2 HOH HOH . KA 4 HOH K 1 401 47 HOH HOH . KA 4 HOH K 2 402 1 HOH HOH . KA 4 HOH K 3 403 3 HOH HOH . KA 4 HOH K 4 404 12 HOH HOH . LA 4 HOH L 1 301 8 HOH HOH . LA 4 HOH L 2 302 5 HOH HOH . LA 4 HOH L 3 303 7 HOH HOH . LA 4 HOH L 4 304 6 HOH HOH . LA 4 HOH L 5 305 10 HOH HOH . LA 4 HOH L 6 306 11 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 . . . N 3 5.826 -50.527 44.71 1 44.81 ? N1 UDP 300 B 1 HETATM 2 C C2 UDP . . . N 3 5.823 -49.487 43.802 1 47.65 ? C2 UDP 300 B 1 HETATM 3 N N3 UDP . . . N 3 4.796 -48.589 43.947 1 40.12 ? N3 UDP 300 B 1 HETATM 4 C C4 UDP . . . N 3 3.792 -48.627 44.894 1 39.56 ? C4 UDP 300 B 1 HETATM 5 C C5 UDP . . . N 3 3.863 -49.734 45.798 1 43.18 ? C5 UDP 300 B 1 HETATM 6 C C6 UDP . . . N 3 4.857 -50.632 45.681 1 45.17 ? C6 UDP 300 B 1 HETATM 7 O O2 UDP . . . N 3 6.67 -49.366 42.928 1 62.31 ? O2 UDP 300 B 1 HETATM 8 O O4 UDP . . . N 3 2.926 -47.738 44.905 1 42.67 ? O4 UDP 300 B 1 HETATM 9 C C1' UDP . . . N 3 6.903 -51.523 44.598 1 44.27 ? C1' UDP 300 B 1 HETATM 10 C C2' UDP . . . N 3 8.152 -51.172 45.415 1 52.74 ? C2' UDP 300 B 1 HETATM 11 O O2' UDP . . . N 3 9.311 -51.594 44.706 1 54.88 ? O2' UDP 300 B 1 HETATM 12 C C3' UDP . . . N 3 7.939 -51.995 46.685 1 54.68 ? C3' UDP 300 B 1 HETATM 13 C C4' UDP . . . N 3 7.272 -53.249 46.136 1 51.57 ? C4' UDP 300 B 1 HETATM 14 O O4' UDP . . . N 3 6.421 -52.77 45.074 1 43.19 ? O4' UDP 300 B 1 HETATM 15 O O3' UDP . . . N 3 9.166 -52.297 47.344 1 51.25 ? O3' UDP 300 B 1 HETATM 16 C C5' UDP . . . N 3 6.46 -54.046 47.126 1 53.91 ? C5' UDP 300 B 1 HETATM 17 O O5' UDP . . . N 3 5.917 -53.155 48.122 1 54.89 ? O5' UDP 300 B 1 HETATM 18 P PA UDP . . . N 3 6.418 -53.191 49.621 1 55.96 ? PA UDP 300 B 1 HETATM 19 O O1A UDP . . . N 3 7.893 -53.046 49.585 1 52.44 -1 O1A UDP 300 B 1 HETATM 20 O O2A UDP . . . N 3 5.636 -52.197 50.484 1 59.08 ? O2A UDP 300 B 1 HETATM 21 O O3A UDP . . . N 3 6.019 -54.653 50.148 0.9 62.68 ? O3A UDP 300 B 1 HETATM 22 P PB UDP . . . N 3 5.913 -55.12 51.66 0.9 59.33 ? PB UDP 300 B 1 HETATM 23 O O1B UDP . . . N 3 4.972 -56.327 51.581 0.9 61.16 -1 O1B UDP 300 B 1 HETATM 24 O O2B UDP . . . N 3 7.337 -55.583 51.979 0.9 55.61 ? O2B UDP 300 B 1 HETATM 25 O O3B UDP . . . N 3 5.414 -54.025 52.563 0.9 54.72 ? O3B UDP 300 B 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 32 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 249 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #