data_4D11 # _model_server_result.job_id yX2wqwBCgOCKhPo0CjSBiQ _model_server_result.datetime_utc '2024-11-08 21:59:47' _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 4d11 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"AA","auth_seq_id":1364}' # _entry.id 4D11 # _exptl.entry_id 4D11 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 6 _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 4D11 _cell.length_a 116.771 _cell.length_b 120.898 _cell.length_c 249.607 _cell.Z_PDB 20 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4D11 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 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 tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 PISA monomeric 1 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,B,I,K,L,M,N,O,P,Q 1 1 D,E,H,J,T,U,V,W,X,Y 2 1 C,G,R,S 3 1 F,Z,AA 4 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 ? 6 N N N ? 6 Q N N ? 6 S N N ? 6 U N N ? 6 Y N N ? 6 AA N 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 126 A CYS 126 1_555 A SG CYS 354 A CYS 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.087 ? disulf ? disulf2 A SG CYS 345 A CYS 345 1_555 A SG CYS 423 A CYS 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf3 A SG CYS 456 A CYS 456 1_555 A SG CYS 473 A CYS 473 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? disulf ? disulf4 A SG CYS 496 A CYS 496 1_555 A SG CYS 513 A CYS 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? disulf ? disulf5 A SG CYS 539 A CYS 539 1_555 A SG CYS 555 A CYS 555 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? disulf ? disulf6 B SG CYS 126 B CYS 126 1_555 B SG CYS 354 B CYS 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? disulf ? disulf7 B SG CYS 345 B CYS 345 1_555 B SG CYS 423 B CYS 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf8 B SG CYS 456 B CYS 456 1_555 B SG CYS 473 B CYS 473 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? disulf ? disulf9 B SG CYS 496 B CYS 496 1_555 B SG CYS 513 B CYS 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? disulf ? disulf10 B SG CYS 539 B CYS 539 1_555 B SG CYS 555 B CYS 555 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? disulf ? disulf11 C SG CYS 126 C CYS 126 1_555 C SG CYS 354 C CYS 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? disulf ? disulf12 C SG CYS 345 C CYS 345 1_555 C SG CYS 423 C CYS 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf13 C SG CYS 456 C CYS 456 1_555 C SG CYS 473 C CYS 473 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf14 C SG CYS 496 C CYS 496 1_555 C SG CYS 513 C CYS 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.067 ? disulf ? disulf15 D SG CYS 126 D CYS 126 1_555 D SG CYS 354 D CYS 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf16 D SG CYS 345 D CYS 345 1_555 D SG CYS 423 D CYS 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf17 D SG CYS 456 D CYS 456 1_555 D SG CYS 473 D CYS 473 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? disulf ? disulf18 D SG CYS 496 D CYS 496 1_555 D SG CYS 513 D CYS 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? disulf ? disulf19 D SG CYS 539 D CYS 539 1_555 D SG CYS 555 D CYS 555 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? disulf ? disulf20 E SG CYS 126 E CYS 126 1_555 E SG CYS 354 E CYS 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? disulf ? disulf21 E SG CYS 345 E CYS 345 1_555 E SG CYS 423 E CYS 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf22 E SG CYS 456 E CYS 456 1_555 E SG CYS 473 E CYS 473 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? disulf ? disulf23 E SG CYS 496 E CYS 496 1_555 E SG CYS 513 E CYS 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.096 ? disulf ? disulf24 E SG CYS 539 E CYS 539 1_555 E SG CYS 555 E CYS 555 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? disulf ? disulf25 F SG CYS 126 F CYS 126 1_555 F SG CYS 354 F CYS 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc1 A OD2 ASP 224 A ASP 224 1_555 L MN MN . A MN 1570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.814 ? metalc ? metalc2 A NE2 HIS 226 A HIS 226 1_555 L MN MN . A MN 1570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? metalc ? metalc3 A NE2 HIS 359 A HIS 359 1_555 L MN MN . A MN 1570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc4 L MN MN . A MN 1570 1_555 N O3B UDP . A UDP 1572 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.098 ? metalc ? metalc5 L MN MN . A MN 1570 1_555 N O2A UDP . A UDP 1572 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.78 ? metalc ? metalc6 B OD2 ASP 224 B ASP 224 1_555 O MN MN . B MN 1571 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.816 ? metalc ? metalc7 B NE2 HIS 226 B HIS 226 1_555 O MN MN . B MN 1571 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc8 B NE2 HIS 359 B HIS 359 1_555 O MN MN . B MN 1571 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc9 O MN MN . B MN 1571 1_555 Q O3B UDP . B UDP 1573 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.001 ? metalc ? metalc10 C OD2 ASP 224 C ASP 224 1_555 R MN MN . C MN 1570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.746 ? metalc ? metalc11 C NE2 HIS 226 C HIS 226 1_555 R MN MN . C MN 1570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc12 C NE2 HIS 359 C HIS 359 1_555 R MN MN . C MN 1570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.244 ? metalc ? metalc13 R MN MN . C MN 1570 1_555 S O2A UDP . C UDP 1571 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc14 R MN MN . C MN 1570 1_555 S O3B UDP . C UDP 1571 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? metalc ? metalc15 D OD2 ASP 224 D ASP 224 1_555 T MN MN . D MN 1570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.876 ? metalc ? metalc16 D NE2 HIS 226 D HIS 226 1_555 T MN MN . D MN 1570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc17 D NE2 HIS 359 D HIS 359 1_555 T MN MN . D MN 1570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc18 T MN MN . D MN 1570 1_555 U O3B UDP . D UDP 1571 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? metalc ? metalc19 T MN MN . D MN 1570 1_555 U O2A UDP . D UDP 1571 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.975 ? metalc ? metalc20 E OD2 ASP 224 E ASP 224 1_555 W MN MN . E MN 1570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.772 ? metalc ? metalc21 E NE2 HIS 226 E HIS 226 1_555 W MN MN . E MN 1570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? metalc ? metalc22 E NE2 HIS 359 E HIS 359 1_555 W MN MN . E MN 1570 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc23 W MN MN . E MN 1570 1_555 Y O2A UDP . E UDP 1572 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.965 ? metalc ? metalc24 W MN MN . E MN 1570 1_555 Y O3B UDP . E UDP 1572 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.621 ? metalc ? metalc25 F OD2 ASP 224 F ASP 224 1_555 Z MN MN . F MN 1363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.844 ? metalc ? metalc26 F NE2 HIS 226 F HIS 226 1_555 Z MN MN . F MN 1363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc27 F NE2 HIS 359 F HIS 359 1_555 Z MN MN . F MN 1363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc28 Z MN MN . F MN 1363 1_555 AA O2A UDP . F UDP 1364 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.797 ? metalc ? metalc29 Z MN MN . F MN 1363 1_555 AA O3B UDP . F UDP 1364 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.609 ? # _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 386 n n N1 C6 UDP sing 387 n n N1 C1' UDP sing 388 n n C2 N3 UDP sing 389 n n C2 O2 UDP doub 390 n n N3 C4 UDP sing 391 n n N3 HN3 UDP sing 392 n n C4 C5 UDP sing 393 n n C4 O4 UDP doub 394 n n C5 C6 UDP doub 395 n n C5 H5 UDP sing 396 n n C6 H6 UDP sing 397 n n C1' C2' UDP sing 398 n n C1' O4' UDP sing 399 n n C1' H1' UDP sing 400 n n C2' O2' UDP sing 401 n n C2' C3' UDP sing 402 n n C2' H2' UDP sing 403 n n O2' HO2' UDP sing 404 n n C3' C4' UDP sing 405 n n C3' O3' UDP sing 406 n n C3' H3' UDP sing 407 n n C4' O4' UDP sing 408 n n C4' C5' UDP sing 409 n n C4' H4' UDP sing 410 n n O3' HO3' UDP sing 411 n n C5' O5' UDP sing 412 n n C5' "H5'1" UDP sing 413 n n C5' "H5'2" UDP sing 414 n n O5' PA UDP sing 415 n n PA O1A UDP doub 416 n n PA O2A UDP sing 417 n n PA O3A UDP sing 418 n n O2A HOA2 UDP sing 419 n n O3A PB UDP sing 420 n n PB O1B UDP doub 421 n n PB O2B UDP sing 422 n n PB O3B UDP sing 423 n n O2B HOB2 UDP sing 424 n n O3B HOB3 UDP sing 425 n n # _atom_sites.entry_id 4D11 _atom_sites.fract_transf_matrix[1][1] 0.008564 _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] 0.008271 _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] 0.004006 _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 L 4 MN A 1 1570 1570 MN MN . M 5 BBK A 1 1571 1571 BBK BBK . N 6 UDP A 1 1572 1572 UDP UDP . O 4 MN B 1 1571 1571 MN MN . P 5 BBK B 1 1572 1572 BBK BBK . Q 6 UDP B 1 1573 1573 UDP UDP . R 4 MN C 1 1570 1570 MN MN . S 6 UDP C 1 1571 1571 UDP UDP . T 4 MN D 1 1570 1570 MN MN . U 6 UDP D 1 1571 1571 UDP UDP . V 5 BBK D 1 1572 1572 BBK BBK . W 4 MN E 1 1570 1570 MN MN . X 5 BBK E 1 1571 1571 BBK BBK . Y 6 UDP E 1 1572 1572 UDP UDP . Z 4 MN F 1 1363 1363 MN MN . AA 6 UDP F 1 1364 1364 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 . . . AA 6 112.795 102.099 -35.672 1 143.87 ? N1 UDP 1364 F 1 HETATM 2 C C2 UDP . . . AA 6 113.741 102.279 -36.616 1 134.96 ? C2 UDP 1364 F 1 HETATM 3 N N3 UDP . . . AA 6 114.286 101.218 -37.251 1 144.44 ? N3 UDP 1364 F 1 HETATM 4 C C4 UDP . . . AA 6 113.903 99.956 -36.952 1 150.46 ? C4 UDP 1364 F 1 HETATM 5 C C5 UDP . . . AA 6 112.94 99.748 -35.983 1 144.49 ? C5 UDP 1364 F 1 HETATM 6 C C6 UDP . . . AA 6 112.401 100.85 -35.343 1 147.95 ? C6 UDP 1364 F 1 HETATM 7 O O2 UDP . . . AA 6 114.128 103.427 -36.932 1 108.73 ? O2 UDP 1364 F 1 HETATM 8 O O4 UDP . . . AA 6 114.405 98.975 -37.539 1 177.44 ? O4 UDP 1364 F 1 HETATM 9 C C1' UDP . . . AA 6 112.254 103.287 -34.979 1 150.41 ? C1' UDP 1364 F 1 HETATM 10 C C2' UDP . . . AA 6 110.755 103.287 -34.676 1 146.76 ? C2' UDP 1364 F 1 HETATM 11 O O2' UDP . . . AA 6 110.027 104.133 -35.579 1 146.16 ? O2' UDP 1364 F 1 HETATM 12 C C3' UDP . . . AA 6 110.681 103.782 -33.242 1 146.5 ? C3' UDP 1364 F 1 HETATM 13 C C4' UDP . . . AA 6 112.038 103.456 -32.62 1 138.79 ? C4' UDP 1364 F 1 HETATM 14 O O4' UDP . . . AA 6 112.946 103.409 -33.717 1 151.5 ? O4' UDP 1364 F 1 HETATM 15 O O3' UDP . . . AA 6 110.432 105.201 -33.205 1 160.33 ? O3' UDP 1364 F 1 HETATM 16 C C5' UDP . . . AA 6 112.177 102.107 -31.925 1 128.16 ? C5' UDP 1364 F 1 HETATM 17 O O5' UDP . . . AA 6 111.32 101.997 -30.804 1 125.41 ? O5' UDP 1364 F 1 HETATM 18 P PA UDP . . . AA 6 109.98 101.13 -30.97 1 126.25 ? PA UDP 1364 F 1 HETATM 19 O O1A UDP . . . AA 6 110.023 100.416 -32.299 1 134.03 ? O1A UDP 1364 F 1 HETATM 20 O O2A UDP . . . AA 6 108.811 102.038 -30.669 1 122.16 ? O2A UDP 1364 F 1 HETATM 21 O O3A UDP . . . AA 6 110.162 100.034 -29.808 1 119.22 ? O3A UDP 1364 F 1 HETATM 22 P PB UDP . . . AA 6 109.392 100.259 -28.417 1 129.22 ? PB UDP 1364 F 1 HETATM 23 O O1B UDP . . . AA 6 110.215 99.285 -27.438 1 107.21 ? O1B UDP 1364 F 1 HETATM 24 O O2B UDP . . . AA 6 107.965 99.762 -28.592 1 122.9 ? O2B UDP 1364 F 1 HETATM 25 O O3B UDP . . . AA 6 109.684 101.676 -27.956 1 134.3 ? O3B UDP 1364 F 1 # _model_server_stats.io_time_ms 42 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 222 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #