data_8UJF # _model_server_result.job_id 7o-iDiGwRu51YvERz8YYBg _model_server_result.datetime_utc '2024-11-23 07:24:22' _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 8ujf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":701}' # _entry.id 8UJF # _exptl.entry_id 8UJF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 404.161 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 8UJF _cell.length_a 66.233 _cell.length_b 123.693 _cell.length_c 165.724 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8UJF _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 G 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 96 A CYS 168 1_555 A SG CYS 337 A CYS 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf2 A SG CYS 250 A CYS 322 1_555 A SG CYS 334 A CYS 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 A SG CYS 328 A CYS 400 1_555 A SG CYS 404 A CYS 476 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf4 A SG CYS 440 A CYS 512 1_555 A SG CYS 458 A CYS 530 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf5 A SG CYS 484 A CYS 556 1_555 A SG CYS 494 A CYS 566 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf6 A SG CYS 518 A CYS 590 1_555 A SG CYS 531 A CYS 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf7 B SG CYS 96 B CYS 168 1_555 B SG CYS 337 B CYS 409 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf8 B SG CYS 250 B CYS 322 1_555 B SG CYS 334 B CYS 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf9 B SG CYS 328 B CYS 400 1_555 B SG CYS 404 B CYS 476 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf10 B SG CYS 440 B CYS 512 1_555 B SG CYS 458 B CYS 530 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf11 B SG CYS 484 B CYS 556 1_555 B SG CYS 494 B CYS 566 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf12 B SG CYS 518 B CYS 590 1_555 B SG CYS 531 B CYS 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? metalc ? metalc1 A OD2 ASP 204 A ASP 276 1_555 E MN MN . A MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc2 A NE2 HIS 206 A HIS 278 1_555 E MN MN . A MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.286 ? metalc ? metalc3 A NE2 HIS 261 A HIS 333 1_555 F MN MN . A MN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? metalc ? metalc4 A OE1 GLU 264 A GLU 336 1_555 F MN MN . A MN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.162 ? metalc ? metalc5 A OE2 GLU 264 A GLU 336 1_555 F MN MN . A MN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.43 ? metalc ? metalc6 A NE2 HIS 342 A HIS 414 1_555 E MN MN . A MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc7 D O3A UDP . A UDP 701 1_555 E MN MN . A MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.574 ? metalc ? metalc8 D PB UDP . A UDP 701 1_555 E MN MN . A MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.593 ? metalc ? metalc9 D O1B UDP . A UDP 701 1_555 E MN MN . A MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.395 ? metalc ? metalc10 D O2B UDP . A UDP 701 1_555 E MN MN . A MN 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.364 ? metalc ? metalc11 F MN MN . A MN 703 1_555 K O HOH . A HOH 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? metalc ? metalc12 F MN MN . A MN 703 1_555 K O HOH . A HOH 806 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.186 ? metalc ? metalc13 B OD2 ASP 204 B ASP 276 1_555 I MN MN . B MN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc14 B NE2 HIS 206 B HIS 278 1_555 I MN MN . B MN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc15 B NE2 HIS 261 B HIS 333 1_555 J MN MN . B MN 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.337 ? metalc ? metalc16 B OE1 GLU 264 B GLU 336 1_555 J MN MN . B MN 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc17 B OE2 GLU 264 B GLU 336 1_555 J MN MN . B MN 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc18 B NE2 HIS 342 B HIS 414 1_555 I MN MN . B MN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc19 G O1A UDP . B UDP 701 1_555 I MN MN . B MN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc20 G O1B UDP . B UDP 701 1_555 I MN MN . B MN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? metalc ? metalc21 G O2B UDP . B UDP 701 1_555 I MN MN . B MN 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.669 ? metalc ? metalc22 I MN MN . B MN 703 1_555 L O HOH . B HOH 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc23 J MN MN . B MN 704 1_555 L O HOH . B HOH 805 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.253 ? metalc ? metalc24 J MN MN . B MN 704 1_555 L O HOH . B HOH 810 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.256 ? # _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 388 n n N1 C6 UDP sing 389 n n N1 C1' UDP sing 390 n n C2 N3 UDP sing 391 n n C2 O2 UDP doub 392 n n N3 C4 UDP sing 393 n n N3 HN3 UDP sing 394 n n C4 C5 UDP sing 395 n n C4 O4 UDP doub 396 n n C5 C6 UDP doub 397 n n C5 H5 UDP sing 398 n n C6 H6 UDP sing 399 n n C1' C2' UDP sing 400 n n C1' O4' UDP sing 401 n n C1' H1' UDP sing 402 n n C2' O2' UDP sing 403 n n C2' C3' UDP sing 404 n n C2' H2' UDP sing 405 n n O2' HO2' UDP sing 406 n n C3' C4' UDP sing 407 n n C3' O3' UDP sing 408 n n C3' H3' UDP sing 409 n n C4' O4' UDP sing 410 n n C4' C5' UDP sing 411 n n C4' H4' UDP sing 412 n n O3' HO3' UDP sing 413 n n C5' O5' UDP sing 414 n n C5' "H5'1" UDP sing 415 n n C5' "H5'2" UDP sing 416 n n O5' PA UDP sing 417 n n PA O1A UDP doub 418 n n PA O2A UDP sing 419 n n PA O3A UDP sing 420 n n O2A HOA2 UDP sing 421 n n O3A PB UDP sing 422 n n PB O1B UDP doub 423 n n PB O2B UDP sing 424 n n PB O3B UDP sing 425 n n O2B HOB2 UDP sing 426 n n O3B HOB3 UDP sing 427 n n # _atom_sites.entry_id 8UJF _atom_sites.fract_transf_matrix[1][1] 0.015098 _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] 0.008085 _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] 0.006034 _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 D 3 UDP A 1 701 701 UDP UDP . E 4 MN A 1 702 1 MN MN . F 4 MN A 1 703 3 MN MN . G 3 UDP B 1 701 701 UDP UDP . H 5 NAG B 1 702 801 NAG NAG . I 4 MN B 1 703 2 MN MN . J 4 MN B 1 704 4 MN MN . K 6 HOH A 1 801 29 HOH HOH . K 6 HOH A 2 802 38 HOH HOH . K 6 HOH A 3 803 33 HOH HOH . K 6 HOH A 4 804 13 HOH HOH . K 6 HOH A 5 805 17 HOH HOH . K 6 HOH A 6 806 16 HOH HOH . K 6 HOH A 7 807 27 HOH HOH . K 6 HOH A 8 808 26 HOH HOH . K 6 HOH A 9 809 32 HOH HOH . K 6 HOH A 10 810 24 HOH HOH . K 6 HOH A 11 811 28 HOH HOH . L 6 HOH B 1 801 31 HOH HOH . L 6 HOH B 2 802 34 HOH HOH . L 6 HOH B 3 803 35 HOH HOH . L 6 HOH B 4 804 36 HOH HOH . L 6 HOH B 5 805 18 HOH HOH . L 6 HOH B 6 806 15 HOH HOH . L 6 HOH B 7 807 40 HOH HOH . L 6 HOH B 8 808 41 HOH HOH . L 6 HOH B 9 809 14 HOH HOH . L 6 HOH B 10 810 19 HOH HOH . L 6 HOH B 11 811 11 HOH HOH . L 6 HOH B 12 812 30 HOH HOH . L 6 HOH B 13 813 23 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 . . . G 3 47.079 -9.77 15.031 1 46.81 ? N1 UDP 701 B 1 HETATM 2 C C2 UDP . . . G 3 47.43 -8.959 16.096 1 48.72 ? C2 UDP 701 B 1 HETATM 3 N N3 UDP . . . G 3 47.079 -7.636 15.963 1 42.6 ? N3 UDP 701 B 1 HETATM 4 C C4 UDP . . . G 3 46.42 -7.062 14.893 1 45.92 ? C4 UDP 701 B 1 HETATM 5 C C5 UDP . . . G 3 46.087 -7.967 13.835 1 48.26 ? C5 UDP 701 B 1 HETATM 6 C C6 UDP . . . G 3 46.417 -9.267 13.935 1 53.38 ? C6 UDP 701 B 1 HETATM 7 O O2 UDP . . . G 3 48.015 -9.379 17.085 1 48.7 ? O2 UDP 701 B 1 HETATM 8 O O4 UDP . . . G 3 46.167 -5.848 14.911 1 48.25 ? O4 UDP 701 B 1 HETATM 9 C C1' UDP . . . G 3 47.415 -11.199 15.132 1 50 ? C1' UDP 701 B 1 HETATM 10 C C2' UDP . . . G 3 46.282 -12.132 14.716 1 59.95 ? C2' UDP 701 B 1 HETATM 11 O O2' UDP . . . G 3 45.322 -12.343 15.747 1 46 ? O2' UDP 701 B 1 HETATM 12 C C3' UDP . . . G 3 47.065 -13.408 14.385 1 43.64 ? C3' UDP 701 B 1 HETATM 13 C C4' UDP . . . G 3 48.404 -12.876 13.859 1 59.76 ? C4' UDP 701 B 1 HETATM 14 O O4' UDP . . . G 3 48.473 -11.483 14.245 1 55.28 ? O4' UDP 701 B 1 HETATM 15 O O3' UDP . . . G 3 47.264 -14.218 15.541 1 21.89 ? O3' UDP 701 B 1 HETATM 16 C C5' UDP . . . G 3 48.591 -12.995 12.366 1 58.46 ? C5' UDP 701 B 1 HETATM 17 O O5' UDP . . . G 3 47.458 -12.399 11.698 1 75.87 ? O5' UDP 701 B 1 HETATM 18 P PA UDP . . . G 3 46.398 -13.283 10.921 1 57.74 ? PA UDP 701 B 1 HETATM 19 O O1A UDP . . . G 3 46.569 -14.678 11.391 1 61.39 -1 O1A UDP 701 B 1 HETATM 20 O O2A UDP . . . G 3 44.999 -12.679 11.025 1 56.05 ? O2A UDP 701 B 1 HETATM 21 O O3A UDP . . . G 3 46.819 -13.162 9.39 1 80.71 ? O3A UDP 701 B 1 HETATM 22 P PB UDP . . . G 3 46.517 -14.261 8.288 1 75.09 ? PB UDP 701 B 1 HETATM 23 O O1B UDP . . . G 3 47.67 -15.253 8.466 1 94.22 ? O1B UDP 701 B 1 HETATM 24 O O2B UDP . . . G 3 45.224 -14.908 8.788 1 79.56 -1 O2B UDP 701 B 1 HETATM 25 O O3B UDP . . . G 3 46.418 -13.669 6.914 1 39.88 ? O3B UDP 701 B 1 HETATM 26 H HN3 UDP . . . G 3 47.291 -7.113 16.612 1 51.12 ? HN3 UDP 701 B 1 HETATM 27 H H5 UDP . . . G 3 45.641 -7.655 13.081 1 57.91 ? H5 UDP 701 B 1 HETATM 28 H H6 UDP . . . G 3 46.191 -9.842 13.24 1 64.05 ? H6 UDP 701 B 1 HETATM 29 H H1' UDP . . . G 3 47.684 -11.392 16.044 1 60 ? H1' UDP 701 B 1 HETATM 30 H H2' UDP . . . G 3 45.838 -11.769 13.933 1 71.95 ? H2' UDP 701 B 1 HETATM 31 H HO2' UDP . . . G 3 44.651 -11.832 15.629 1 55.2 ? HO2' UDP 701 B 1 HETATM 32 H H3' UDP . . . G 3 46.609 -13.902 13.685 1 52.37 ? H3' UDP 701 B 1 HETATM 33 H H4' UDP . . . G 3 49.118 -13.343 14.32 1 71.71 ? H4' UDP 701 B 1 HETATM 34 H "H5'1" UDP . . . G 3 48.656 -13.931 12.119 1 70.15 ? "H5'1" UDP 701 B 1 HETATM 35 H "H5'2" UDP . . . G 3 49.402 -12.534 12.1 1 70.15 ? "H5'2" UDP 701 B 1 # _model_server_stats.io_time_ms 192 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 248 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 35 #