data_4L5B # _model_server_result.job_id HYOJ0icMLDGFYNadbmu_Mw _model_server_result.datetime_utc '2025-03-04 05:27:02' _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 4l5b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":302}' # _entry.id 4L5B # _exptl.entry_id 4L5B _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 4L5B _cell.length_a 68.671 _cell.length_b 68.671 _cell.length_c 120.019 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4L5B _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 _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 F 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 421 n n N1 C6 UDP sing 422 n n N1 C1' UDP sing 423 n n C2 N3 UDP sing 424 n n C2 O2 UDP doub 425 n n N3 C4 UDP sing 426 n n N3 HN3 UDP sing 427 n n C4 C5 UDP sing 428 n n C4 O4 UDP doub 429 n n C5 C6 UDP doub 430 n n C5 H5 UDP sing 431 n n C6 H6 UDP sing 432 n n C1' C2' UDP sing 433 n n C1' O4' UDP sing 434 n n C1' H1' UDP sing 435 n n C2' O2' UDP sing 436 n n C2' C3' UDP sing 437 n n C2' H2' UDP sing 438 n n O2' HO2' UDP sing 439 n n C3' C4' UDP sing 440 n n C3' O3' UDP sing 441 n n C3' H3' UDP sing 442 n n C4' O4' UDP sing 443 n n C4' C5' UDP sing 444 n n C4' H4' UDP sing 445 n n O3' HO3' UDP sing 446 n n C5' O5' UDP sing 447 n n C5' "H5'1" UDP sing 448 n n C5' "H5'2" UDP sing 449 n n O5' PA UDP sing 450 n n PA O1A UDP doub 451 n n PA O2A UDP sing 452 n n PA O3A UDP sing 453 n n O2A HOA2 UDP sing 454 n n O3A PB UDP sing 455 n n PB O1B UDP doub 456 n n PB O2B UDP sing 457 n n PB O3B UDP sing 458 n n O2B HOB2 UDP sing 459 n n O3B HOB3 UDP sing 460 n n # _atom_sites.entry_id 4L5B _atom_sites.fract_transf_matrix[1][1] 0.014562 _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] 0.014562 _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] 0.008332 _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 1UX A 1 301 301 1UX 1UX . D 3 UDP A 1 302 401 UDP UDP . E 2 1UX B 1 301 301 1UX 1UX . F 3 UDP B 1 302 401 UDP UDP . G 4 HOH A 1 401 1 HOH HOH . G 4 HOH A 2 402 2 HOH HOH . G 4 HOH A 3 403 3 HOH HOH . G 4 HOH A 4 404 4 HOH HOH . G 4 HOH A 5 405 9 HOH HOH . G 4 HOH A 6 406 10 HOH HOH . G 4 HOH A 7 407 12 HOH HOH . G 4 HOH A 8 408 13 HOH HOH . G 4 HOH A 9 409 15 HOH HOH . G 4 HOH A 10 410 16 HOH HOH . G 4 HOH A 11 411 19 HOH HOH . G 4 HOH A 12 412 21 HOH HOH . G 4 HOH A 13 413 22 HOH HOH . G 4 HOH A 14 414 26 HOH HOH . G 4 HOH A 15 415 27 HOH HOH . G 4 HOH A 16 416 28 HOH HOH . G 4 HOH A 17 417 29 HOH HOH . G 4 HOH A 18 418 33 HOH HOH . G 4 HOH A 19 419 36 HOH HOH . G 4 HOH A 20 420 37 HOH HOH . G 4 HOH A 21 421 38 HOH HOH . G 4 HOH A 22 422 40 HOH HOH . G 4 HOH A 23 423 41 HOH HOH . G 4 HOH A 24 424 43 HOH HOH . G 4 HOH A 25 425 45 HOH HOH . G 4 HOH A 26 426 46 HOH HOH . G 4 HOH A 27 427 47 HOH HOH . G 4 HOH A 28 428 51 HOH HOH . G 4 HOH A 29 429 53 HOH HOH . G 4 HOH A 30 430 54 HOH HOH . G 4 HOH A 31 431 55 HOH HOH . G 4 HOH A 32 432 56 HOH HOH . G 4 HOH A 33 433 57 HOH HOH . G 4 HOH A 34 434 58 HOH HOH . G 4 HOH A 35 435 59 HOH HOH . G 4 HOH A 36 436 60 HOH HOH . G 4 HOH A 37 437 61 HOH HOH . G 4 HOH A 38 438 62 HOH HOH . G 4 HOH A 39 439 72 HOH HOH . G 4 HOH A 40 440 64 HOH HOH . H 4 HOH B 1 401 5 HOH HOH . H 4 HOH B 2 402 6 HOH HOH . H 4 HOH B 3 403 7 HOH HOH . H 4 HOH B 4 404 8 HOH HOH . H 4 HOH B 5 405 11 HOH HOH . H 4 HOH B 6 406 14 HOH HOH . H 4 HOH B 7 407 17 HOH HOH . H 4 HOH B 8 408 18 HOH HOH . H 4 HOH B 9 409 20 HOH HOH . H 4 HOH B 10 410 23 HOH HOH . H 4 HOH B 11 411 24 HOH HOH . H 4 HOH B 12 412 25 HOH HOH . H 4 HOH B 13 413 30 HOH HOH . H 4 HOH B 14 414 31 HOH HOH . H 4 HOH B 15 415 32 HOH HOH . H 4 HOH B 16 416 34 HOH HOH . H 4 HOH B 17 417 35 HOH HOH . H 4 HOH B 18 418 39 HOH HOH . H 4 HOH B 19 419 42 HOH HOH . H 4 HOH B 20 420 44 HOH HOH . H 4 HOH B 21 421 48 HOH HOH . H 4 HOH B 22 422 49 HOH HOH . H 4 HOH B 23 423 50 HOH HOH . H 4 HOH B 24 424 52 HOH HOH . H 4 HOH B 25 425 63 HOH HOH . H 4 HOH B 26 426 65 HOH HOH . H 4 HOH B 27 427 66 HOH HOH . H 4 HOH B 28 428 67 HOH HOH . H 4 HOH B 29 429 68 HOH HOH . H 4 HOH B 30 430 69 HOH HOH . H 4 HOH B 31 431 70 HOH HOH . H 4 HOH B 32 432 71 HOH HOH . H 4 HOH B 33 433 73 HOH HOH . H 4 HOH B 34 434 74 HOH HOH . H 4 HOH B 35 435 75 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 . . . D 3 -25.036 29.348 2.541 1 49.4 ? N1 UDP 302 A 1 HETATM 2 C C2 UDP . . . D 3 -25.021 30.693 3.003 1 53.88 ? C2 UDP 302 A 1 HETATM 3 N N3 UDP . . . D 3 -24.177 31.028 3.99 1 54.99 ? N3 UDP 302 A 1 HETATM 4 C C4 UDP . . . D 3 -23.356 30.114 4.533 1 56.53 ? C4 UDP 302 A 1 HETATM 5 C C5 UDP . . . D 3 -23.367 28.786 4.101 1 55.69 ? C5 UDP 302 A 1 HETATM 6 C C6 UDP . . . D 3 -24.234 28.416 3.081 1 49.42 ? C6 UDP 302 A 1 HETATM 7 O O2 UDP . . . D 3 -25.775 31.571 2.499 1 48.87 ? O2 UDP 302 A 1 HETATM 8 O O4 UDP . . . D 3 -22.59 30.465 5.453 1 58.22 ? O4 UDP 302 A 1 HETATM 9 C C1' UDP . . . D 3 -25.966 29.013 1.492 1 43.86 ? C1' UDP 302 A 1 HETATM 10 C C2' UDP . . . D 3 -25.323 28.855 0.132 1 45.71 ? C2' UDP 302 A 1 HETATM 11 O O2' UDP . . . D 3 -25.142 30.126 -0.507 1 47.71 ? O2' UDP 302 A 1 HETATM 12 C C3' UDP . . . D 3 -26.316 27.909 -0.539 1 48.44 ? C3' UDP 302 A 1 HETATM 13 C C4' UDP . . . D 3 -26.863 27.066 0.605 1 45.84 ? C4' UDP 302 A 1 HETATM 14 O O4' UDP . . . D 3 -26.579 27.773 1.803 1 45.71 ? O4' UDP 302 A 1 HETATM 15 O O3' UDP . . . D 3 -27.427 28.639 -1.071 1 52.94 ? O3' UDP 302 A 1 HETATM 16 C C5' UDP . . . D 3 -26.235 25.692 0.799 1 46.06 ? C5' UDP 302 A 1 HETATM 17 O O5' UDP . . . D 3 -24.808 25.77 0.661 1 49.61 ? O5' UDP 302 A 1 HETATM 18 P PA UDP . . . D 3 -24.078 24.934 -0.498 1 46.49 ? PA UDP 302 A 1 HETATM 19 O O1A UDP . . . D 3 -24.875 25.051 -1.777 1 45.86 ? O1A UDP 302 A 1 HETATM 20 O O2A UDP . . . D 3 -22.619 25.301 -0.572 1 43.08 ? O2A UDP 302 A 1 HETATM 21 O O3A UDP . . . D 3 -24.271 23.539 0.255 1 43.03 ? O3A UDP 302 A 1 HETATM 22 P PB UDP . . . D 3 -23.683 22.086 -0.052 1 43.1 ? PB UDP 302 A 1 HETATM 23 O O1B UDP . . . D 3 -22.764 22.33 -1.243 1 42.95 ? O1B UDP 302 A 1 HETATM 24 O O2B UDP . . . D 3 -24.9 21.249 -0.372 1 39.68 ? O2B UDP 302 A 1 HETATM 25 O O3B UDP . . . D 3 -23.103 21.657 1.257 1 38.29 ? O3B UDP 302 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 243 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 25 #