data_4JLJ # _model_server_result.job_id X-OBJHDSR3CBVsGFMZSBgw _model_server_result.datetime_utc '2024-10-19 11:32:59' _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 4jlj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":303}' # _entry.id 4JLJ # _exptl.entry_id 4JLJ _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 4JLJ _cell.length_a 68.998 _cell.length_b 68.998 _cell.length_c 123.18 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4JLJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 E N N ? 3 H 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 405 n n N1 C6 UDP sing 406 n n N1 C1' UDP sing 407 n n C2 N3 UDP sing 408 n n C2 O2 UDP doub 409 n n N3 C4 UDP sing 410 n n N3 HN3 UDP sing 411 n n C4 C5 UDP sing 412 n n C4 O4 UDP doub 413 n n C5 C6 UDP doub 414 n n C5 H5 UDP sing 415 n n C6 H6 UDP sing 416 n n C1' C2' UDP sing 417 n n C1' O4' UDP sing 418 n n C1' H1' UDP sing 419 n n C2' O2' UDP sing 420 n n C2' C3' UDP sing 421 n n C2' H2' UDP sing 422 n n O2' HO2' UDP sing 423 n n C3' C4' UDP sing 424 n n C3' O3' UDP sing 425 n n C3' H3' UDP sing 426 n n C4' O4' UDP sing 427 n n C4' C5' UDP sing 428 n n C4' H4' UDP sing 429 n n O3' HO3' UDP sing 430 n n C5' O5' UDP sing 431 n n C5' "H5'1" UDP sing 432 n n C5' "H5'2" UDP sing 433 n n O5' PA UDP sing 434 n n PA O1A UDP doub 435 n n PA O2A UDP sing 436 n n PA O3A UDP sing 437 n n O2A HOA2 UDP sing 438 n n O3A PB UDP sing 439 n n PB O1B UDP doub 440 n n PB O2B UDP sing 441 n n PB O3B UDP sing 442 n n O2B HOB2 UDP sing 443 n n O3B HOB3 UDP sing 444 n n # _atom_sites.entry_id 4JLJ _atom_sites.fract_transf_matrix[1][1] 0.014493 _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] 0.014493 _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] 0.008118 _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 C 2 1NM A 1 301 301 1NM DRG . D 2 1NM A 1 302 302 1NM DRG . E 3 UDP A 1 303 401 UDP UDP . F 2 1NM B 1 301 301 1NM DRG . G 2 1NM B 1 302 302 1NM DRG . H 3 UDP B 1 303 401 UDP UDP . I 4 HOH A 1 401 2 HOH HOH . I 4 HOH A 2 402 3 HOH HOH . I 4 HOH A 3 403 5 HOH HOH . I 4 HOH A 4 404 6 HOH HOH . I 4 HOH A 5 405 7 HOH HOH . I 4 HOH A 6 406 9 HOH HOH . I 4 HOH A 7 407 14 HOH HOH . I 4 HOH A 8 408 19 HOH HOH . I 4 HOH A 9 409 21 HOH HOH . I 4 HOH A 10 410 22 HOH HOH . I 4 HOH A 11 411 26 HOH HOH . I 4 HOH A 12 412 27 HOH HOH . I 4 HOH A 13 413 32 HOH HOH . I 4 HOH A 14 414 33 HOH HOH . I 4 HOH A 15 415 34 HOH HOH . I 4 HOH A 16 416 37 HOH HOH . I 4 HOH A 17 417 41 HOH HOH . I 4 HOH A 18 418 46 HOH HOH . I 4 HOH A 19 419 47 HOH HOH . I 4 HOH A 20 420 51 HOH HOH . I 4 HOH A 21 421 52 HOH HOH . I 4 HOH A 22 422 53 HOH HOH . I 4 HOH A 23 423 54 HOH HOH . I 4 HOH A 24 424 63 HOH HOH . I 4 HOH A 25 425 64 HOH HOH . I 4 HOH A 26 426 66 HOH HOH . I 4 HOH A 27 427 68 HOH HOH . I 4 HOH A 28 428 69 HOH HOH . I 4 HOH A 29 429 70 HOH HOH . I 4 HOH A 30 430 71 HOH HOH . I 4 HOH A 31 431 72 HOH HOH . I 4 HOH A 32 432 73 HOH HOH . I 4 HOH A 33 433 75 HOH HOH . I 4 HOH A 34 434 76 HOH HOH . I 4 HOH A 35 435 78 HOH HOH . I 4 HOH A 36 436 83 HOH HOH . I 4 HOH A 37 437 84 HOH HOH . I 4 HOH A 38 438 85 HOH HOH . I 4 HOH A 39 439 86 HOH HOH . I 4 HOH A 40 440 87 HOH HOH . I 4 HOH A 41 441 89 HOH HOH . I 4 HOH A 42 442 90 HOH HOH . I 4 HOH A 43 443 91 HOH HOH . I 4 HOH A 44 444 92 HOH HOH . I 4 HOH A 45 445 93 HOH HOH . I 4 HOH A 46 446 94 HOH HOH . I 4 HOH A 47 447 95 HOH HOH . I 4 HOH A 48 448 96 HOH HOH . I 4 HOH A 49 449 97 HOH HOH . I 4 HOH A 50 450 99 HOH HOH . I 4 HOH A 51 451 103 HOH HOH . I 4 HOH A 52 452 104 HOH HOH . I 4 HOH A 53 453 105 HOH HOH . I 4 HOH A 54 454 106 HOH HOH . I 4 HOH A 55 455 107 HOH HOH . I 4 HOH A 56 456 114 HOH HOH . I 4 HOH A 57 457 115 HOH HOH . I 4 HOH A 58 458 116 HOH HOH . I 4 HOH A 59 459 118 HOH HOH . J 4 HOH B 1 401 1 HOH HOH . J 4 HOH B 2 402 4 HOH HOH . J 4 HOH B 3 403 8 HOH HOH . J 4 HOH B 4 404 10 HOH HOH . J 4 HOH B 5 405 11 HOH HOH . J 4 HOH B 6 406 12 HOH HOH . J 4 HOH B 7 407 13 HOH HOH . J 4 HOH B 8 408 15 HOH HOH . J 4 HOH B 9 409 16 HOH HOH . J 4 HOH B 10 410 17 HOH HOH . J 4 HOH B 11 411 18 HOH HOH . J 4 HOH B 12 412 20 HOH HOH . J 4 HOH B 13 413 23 HOH HOH . J 4 HOH B 14 414 24 HOH HOH . J 4 HOH B 15 415 25 HOH HOH . J 4 HOH B 16 416 28 HOH HOH . J 4 HOH B 17 417 29 HOH HOH . J 4 HOH B 18 418 30 HOH HOH . J 4 HOH B 19 419 31 HOH HOH . J 4 HOH B 20 420 35 HOH HOH . J 4 HOH B 21 421 36 HOH HOH . J 4 HOH B 22 422 38 HOH HOH . J 4 HOH B 23 423 39 HOH HOH . J 4 HOH B 24 424 40 HOH HOH . J 4 HOH B 25 425 42 HOH HOH . J 4 HOH B 26 426 43 HOH HOH . J 4 HOH B 27 427 44 HOH HOH . J 4 HOH B 28 428 45 HOH HOH . J 4 HOH B 29 429 48 HOH HOH . J 4 HOH B 30 430 49 HOH HOH . J 4 HOH B 31 431 50 HOH HOH . J 4 HOH B 32 432 55 HOH HOH . J 4 HOH B 33 433 56 HOH HOH . J 4 HOH B 34 434 57 HOH HOH . J 4 HOH B 35 435 58 HOH HOH . J 4 HOH B 36 436 59 HOH HOH . J 4 HOH B 37 437 60 HOH HOH . J 4 HOH B 38 438 61 HOH HOH . J 4 HOH B 39 439 62 HOH HOH . J 4 HOH B 40 440 65 HOH HOH . J 4 HOH B 41 441 67 HOH HOH . J 4 HOH B 42 442 74 HOH HOH . J 4 HOH B 43 443 77 HOH HOH . J 4 HOH B 44 444 79 HOH HOH . J 4 HOH B 45 445 80 HOH HOH . J 4 HOH B 46 446 81 HOH HOH . J 4 HOH B 47 447 82 HOH HOH . J 4 HOH B 48 448 88 HOH HOH . J 4 HOH B 49 449 98 HOH HOH . J 4 HOH B 50 450 100 HOH HOH . J 4 HOH B 51 451 101 HOH HOH . J 4 HOH B 52 452 102 HOH HOH . J 4 HOH B 53 453 108 HOH HOH . J 4 HOH B 54 454 109 HOH HOH . J 4 HOH B 55 455 110 HOH HOH . J 4 HOH B 56 456 111 HOH HOH . J 4 HOH B 57 457 112 HOH HOH . J 4 HOH B 58 458 113 HOH HOH . J 4 HOH B 59 459 117 HOH HOH . J 4 HOH B 60 460 119 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 . . . H 3 -25.397 -29.069 -30.937 1 52.5 ? N1 UDP 303 B 1 HETATM 2 C C2 UDP . . . H 3 -25.479 -30.109 -31.896 1 54.54 ? C2 UDP 303 B 1 HETATM 3 N N3 UDP . . . H 3 -24.491 -30.305 -32.779 1 54.07 ? N3 UDP 303 B 1 HETATM 4 C C4 UDP . . . H 3 -23.398 -29.522 -32.773 1 54.09 ? C4 UDP 303 B 1 HETATM 5 C C5 UDP . . . H 3 -23.292 -28.484 -31.854 1 55.14 ? C5 UDP 303 B 1 HETATM 6 C C6 UDP . . . H 3 -24.313 -28.28 -30.93 1 54.3 ? C6 UDP 303 B 1 HETATM 7 O O2 UDP . . . H 3 -26.479 -30.86 -31.925 1 53.76 ? O2 UDP 303 B 1 HETATM 8 O O4 UDP . . . H 3 -22.485 -29.711 -33.604 1 50.99 ? O4 UDP 303 B 1 HETATM 9 C C1' UDP . . . H 3 -26.497 -28.866 -29.975 1 47.24 ? C1' UDP 303 B 1 HETATM 10 C C2' UDP . . . H 3 -25.976 -28.916 -28.548 1 44.22 ? C2' UDP 303 B 1 HETATM 11 O O2' UDP . . . H 3 -26.019 -30.252 -28.041 1 46.76 ? O2' UDP 303 B 1 HETATM 12 C C3' UDP . . . H 3 -26.886 -27.94 -27.806 1 45.58 ? C3' UDP 303 B 1 HETATM 13 C C4' UDP . . . H 3 -27.436 -26.998 -28.868 1 41.87 ? C4' UDP 303 B 1 HETATM 14 O O4' UDP . . . H 3 -27.125 -27.583 -30.143 1 42.31 ? O4' UDP 303 B 1 HETATM 15 O O3' UDP . . . H 3 -27.965 -28.633 -27.185 1 49.22 ? O3' UDP 303 B 1 HETATM 16 C C5' UDP . . . H 3 -26.803 -25.621 -28.711 1 39.57 ? C5' UDP 303 B 1 HETATM 17 O O5' UDP . . . H 3 -25.39 -25.755 -28.683 1 36.68 ? O5' UDP 303 B 1 HETATM 18 P PA UDP . . . H 3 -24.422 -24.977 -27.663 1 36.99 ? PA UDP 303 B 1 HETATM 19 O O1A UDP . . . H 3 -23.009 -25.269 -27.965 1 35.32 ? O1A UDP 303 B 1 HETATM 20 O O2A UDP . . . H 3 -24.779 -25.211 -26.238 1 37.06 ? O2A UDP 303 B 1 HETATM 21 O O3A UDP . . . H 3 -24.79 -23.473 -28.125 1 37.94 ? O3A UDP 303 B 1 HETATM 22 P PB UDP . . . H 3 -24.202 -22.079 -27.537 1 36.06 ? PB UDP 303 B 1 HETATM 23 O O1B UDP . . . H 3 -23.766 -21.359 -28.781 1 35.38 ? O1B UDP 303 B 1 HETATM 24 O O2B UDP . . . H 3 -25.325 -21.372 -26.864 1 37.09 ? O2B UDP 303 B 1 HETATM 25 O O3B UDP . . . H 3 -23.131 -22.371 -26.552 1 34.07 ? O3B UDP 303 B 1 # _model_server_stats.io_time_ms 57 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 25 #