data_4X6L # _model_server_result.job_id d6nBGV52mIiNPoZCrpmjqA _model_server_result.datetime_utc '2025-03-21 21:33:55' _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 4x6l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":500}' # _entry.id 4X6L # _exptl.entry_id 4X6L _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 3 _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 120 _cell.entry_id 4X6L _cell.length_a 162.289 _cell.length_b 162.289 _cell.length_c 228.024 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4X6L _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # 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 trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 author_and_software_defined_assembly 2 PISA trimeric 3 author_and_software_defined_assembly 3 PISA trimeric 3 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E 1 1,2,4 B,F 2 1,3,5 C,G 3 1,3,5 D 4 1,2,4 # 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_665 -y+1,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 81.1445 140.546397 0 3 'crystal symmetry operation' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 4 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -81.1445 140.546397 0 5 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 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 E N N ? 2 F N N ? 2 G 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 356 n n N1 C6 UDP sing 357 n n N1 C1' UDP sing 358 n n C2 N3 UDP sing 359 n n C2 O2 UDP doub 360 n n N3 C4 UDP sing 361 n n N3 HN3 UDP sing 362 n n C4 C5 UDP sing 363 n n C4 O4 UDP doub 364 n n C5 C6 UDP doub 365 n n C5 H5 UDP sing 366 n n C6 H6 UDP sing 367 n n C1' C2' UDP sing 368 n n C1' O4' UDP sing 369 n n C1' H1' UDP sing 370 n n C2' O2' UDP sing 371 n n C2' C3' UDP sing 372 n n C2' H2' UDP sing 373 n n O2' HO2' UDP sing 374 n n C3' C4' UDP sing 375 n n C3' O3' UDP sing 376 n n C3' H3' UDP sing 377 n n C4' O4' UDP sing 378 n n C4' C5' UDP sing 379 n n C4' H4' UDP sing 380 n n O3' HO3' UDP sing 381 n n C5' O5' UDP sing 382 n n C5' "H5'1" UDP sing 383 n n C5' "H5'2" UDP sing 384 n n O5' PA UDP sing 385 n n PA O1A UDP doub 386 n n PA O2A UDP sing 387 n n PA O3A UDP sing 388 n n O2A HOA2 UDP sing 389 n n O3A PB UDP sing 390 n n PB O1B UDP doub 391 n n PB O2B UDP sing 392 n n PB O3B UDP sing 393 n n O2B HOB2 UDP sing 394 n n O3B HOB3 UDP sing 395 n n # _atom_sites.entry_id 4X6L _atom_sites.fract_transf_matrix[1][1] 0.006162 _atom_sites.fract_transf_matrix[1][2] 0.003558 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007115 _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] 0.004386 _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 1 500 500 UDP UDP . F 2 UDP B 1 500 500 UDP UDP . G 2 UDP C 1 500 500 UDP UDP . # 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 . . . G 2 38.957 17.868 -65.179 1 115.77 ? N1 UDP 500 C 1 HETATM 2 C C2 UDP . . . G 2 38.275 17.113 -66.12 1 116.24 ? C2 UDP 500 C 1 HETATM 3 N N3 UDP . . . G 2 38.591 15.77 -66.13 1 113.22 ? N3 UDP 500 C 1 HETATM 4 C C4 UDP . . . G 2 39.48 15.12 -65.303 1 110.03 ? C4 UDP 500 C 1 HETATM 5 C C5 UDP . . . G 2 40.091 15.954 -64.303 1 111.43 ? C5 UDP 500 C 1 HETATM 6 C C6 UDP . . . G 2 39.809 17.272 -64.267 1 112.94 ? C6 UDP 500 C 1 HETATM 7 O O2 UDP . . . G 2 37.431 17.582 -66.876 1 119.11 ? O2 UDP 500 C 1 HETATM 8 O O4 UDP . . . G 2 39.72 13.917 -65.491 1 107.12 ? O4 UDP 500 C 1 HETATM 9 C C1' UDP . . . G 2 38.936 19.345 -65.301 1 121.42 ? C1' UDP 500 C 1 HETATM 10 C C2' UDP . . . G 2 39.852 19.878 -66.399 1 125.58 ? C2' UDP 500 C 1 HETATM 11 O O2' UDP . . . G 2 41.231 19.86 -66.053 1 127.07 ? O2' UDP 500 C 1 HETATM 12 C C3' UDP . . . G 2 39.228 21.257 -66.635 1 128.08 ? C3' UDP 500 C 1 HETATM 13 C C4' UDP . . . G 2 37.732 20.966 -66.497 1 128.06 ? C4' UDP 500 C 1 HETATM 14 O O4' UDP . . . G 2 37.634 19.78 -65.66 1 124.44 ? O4' UDP 500 C 1 HETATM 15 O O3' UDP . . . G 2 39.617 22.24 -65.679 1 129.14 ? O3' UDP 500 C 1 HETATM 16 C C5' UDP . . . G 2 36.964 20.789 -67.793 1 130.25 ? C5' UDP 500 C 1 HETATM 17 O O5' UDP . . . G 2 36.875 22.054 -68.512 1 130.45 ? O5' UDP 500 C 1 HETATM 18 P PA UDP . . . G 2 36.175 22.403 -69.916 1 128.16 ? PA UDP 500 C 1 HETATM 19 O O1A UDP . . . G 2 37.137 22.176 -71.027 1 125.56 ? O1A UDP 500 C 1 HETATM 20 O O2A UDP . . . G 2 35.713 23.885 -69.908 1 126.03 ? O2A UDP 500 C 1 HETATM 21 O O3A UDP . . . G 2 34.895 21.468 -70.141 1 127.79 ? O3A UDP 500 C 1 HETATM 22 P PB UDP . . . G 2 33.641 20.924 -69.3 1 123.06 ? PB UDP 500 C 1 HETATM 23 O O1B UDP . . . G 2 32.51 20.718 -70.186 1 122.79 ? O1B UDP 500 C 1 HETATM 24 O O2B UDP . . . G 2 33.205 21.966 -68.25 1 121.64 ? O2B UDP 500 C 1 HETATM 25 O O3B UDP . . . G 2 34.071 19.572 -68.653 1 120.48 ? O3B UDP 500 C 1 # _model_server_stats.io_time_ms 36 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 25 #