data_5HUU # _model_server_result.job_id RH65HUU0knIgVdGdDbZ20g _model_server_result.datetime_utc '2024-11-05 00:31:54' _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 5huu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 5HUU # _exptl.entry_id 5HUU _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 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 120 _cell.entry_id 5HUU _cell.length_a 98.682 _cell.length_b 98.682 _cell.length_c 188.885 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5HUU _symmetry.cell_setting ? _symmetry.Int_Tables_number 172 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 PISA tetrameric 4 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 1 2 A,B,C,D,E,F,G,H 2 1,2 # 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' 4_585 -x,-y+3,z -1 0 0 0 -1 0 0 0 1 -148.023 256.383357 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E 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 387 n n N1 C6 UDP sing 388 n n N1 C1' UDP sing 389 n n C2 N3 UDP sing 390 n n C2 O2 UDP doub 391 n n N3 C4 UDP sing 392 n n N3 HN3 UDP sing 393 n n C4 C5 UDP sing 394 n n C4 O4 UDP doub 395 n n C5 C6 UDP doub 396 n n C5 H5 UDP sing 397 n n C6 H6 UDP sing 398 n n C1' C2' UDP sing 399 n n C1' O4' UDP sing 400 n n C1' H1' UDP sing 401 n n C2' O2' UDP sing 402 n n C2' C3' UDP sing 403 n n C2' H2' UDP sing 404 n n O2' HO2' UDP sing 405 n n C3' C4' UDP sing 406 n n C3' O3' UDP sing 407 n n C3' H3' UDP sing 408 n n C4' O4' UDP sing 409 n n C4' C5' UDP sing 410 n n C4' H4' UDP sing 411 n n O3' HO3' UDP sing 412 n n C5' O5' UDP sing 413 n n C5' "H5'1" UDP sing 414 n n C5' "H5'2" UDP sing 415 n n O5' PA UDP sing 416 n n PA O1A UDP doub 417 n n PA O2A UDP sing 418 n n PA O3A UDP sing 419 n n O2A HOA2 UDP sing 420 n n O3A PB UDP sing 421 n n PB O1B UDP doub 422 n n PB O2B UDP sing 423 n n PB O3B UDP sing 424 n n O2B HOB2 UDP sing 425 n n O3B HOB3 UDP sing 426 n n # _atom_sites.entry_id 5HUU _atom_sites.fract_transf_matrix[1][1] 0.010134 _atom_sites.fract_transf_matrix[1][2] 0.005851 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011701 _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] 0.005294 _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 UDP A 1 501 501 UDP UDP . D 3 G6P A 1 502 502 G6P G6P . E 2 UDP B 1 501 501 UDP UDP . F 3 G6P B 1 502 502 G6P G6P . G 4 HOH A 1 601 12 HOH HOH . G 4 HOH A 2 602 29 HOH HOH . G 4 HOH A 3 603 41 HOH HOH . G 4 HOH A 4 604 35 HOH HOH . G 4 HOH A 5 605 27 HOH HOH . G 4 HOH A 6 606 50 HOH HOH . G 4 HOH A 7 607 40 HOH HOH . G 4 HOH A 8 608 51 HOH HOH . G 4 HOH A 9 609 25 HOH HOH . G 4 HOH A 10 610 8 HOH HOH . G 4 HOH A 11 611 4 HOH HOH . G 4 HOH A 12 612 49 HOH HOH . G 4 HOH A 13 613 9 HOH HOH . G 4 HOH A 14 614 17 HOH HOH . G 4 HOH A 15 615 3 HOH HOH . G 4 HOH A 16 616 14 HOH HOH . G 4 HOH A 17 617 19 HOH HOH . G 4 HOH A 18 618 24 HOH HOH . G 4 HOH A 19 619 15 HOH HOH . G 4 HOH A 20 620 10 HOH HOH . G 4 HOH A 21 621 7 HOH HOH . G 4 HOH A 22 622 16 HOH HOH . G 4 HOH A 23 623 2 HOH HOH . G 4 HOH A 24 624 20 HOH HOH . G 4 HOH A 25 625 43 HOH HOH . G 4 HOH A 26 626 39 HOH HOH . G 4 HOH A 27 627 37 HOH HOH . G 4 HOH A 28 628 48 HOH HOH . G 4 HOH A 29 629 36 HOH HOH . G 4 HOH A 30 630 38 HOH HOH . G 4 HOH A 31 631 30 HOH HOH . H 4 HOH B 1 601 28 HOH HOH . H 4 HOH B 2 602 55 HOH HOH . H 4 HOH B 3 603 42 HOH HOH . H 4 HOH B 4 604 46 HOH HOH . H 4 HOH B 5 605 22 HOH HOH . H 4 HOH B 6 606 34 HOH HOH . H 4 HOH B 7 607 26 HOH HOH . H 4 HOH B 8 608 5 HOH HOH . H 4 HOH B 9 609 18 HOH HOH . H 4 HOH B 10 610 56 HOH HOH . H 4 HOH B 11 611 54 HOH HOH . H 4 HOH B 12 612 6 HOH HOH . H 4 HOH B 13 613 47 HOH HOH . H 4 HOH B 14 614 31 HOH HOH . H 4 HOH B 15 615 21 HOH HOH . H 4 HOH B 16 616 13 HOH HOH . H 4 HOH B 17 617 53 HOH HOH . H 4 HOH B 18 618 45 HOH HOH . H 4 HOH B 19 619 33 HOH HOH . H 4 HOH B 20 620 1 HOH HOH . H 4 HOH B 21 621 32 HOH HOH . H 4 HOH B 22 622 11 HOH HOH . H 4 HOH B 23 623 52 HOH HOH . H 4 HOH B 24 624 23 HOH HOH . H 4 HOH B 25 625 44 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 . . . C 2 -48.965 140.691 12.276 1 45.88 ? N1 UDP 501 A 1 HETATM 2 C C2 UDP . . . C 2 -49.901 140.549 11.164 1 50.21 ? C2 UDP 501 A 1 HETATM 3 N N3 UDP . . . C 2 -51.048 141.444 11.036 1 49.56 ? N3 UDP 501 A 1 HETATM 4 C C4 UDP . . . C 2 -51.263 142.467 11.99 1 48.21 ? C4 UDP 501 A 1 HETATM 5 C C5 UDP . . . C 2 -50.328 142.628 13.109 1 44.69 ? C5 UDP 501 A 1 HETATM 6 C C6 UDP . . . C 2 -49.174 141.721 13.235 1 51.1 ? C6 UDP 501 A 1 HETATM 7 O O2 UDP . . . C 2 -49.729 139.67 10.345 1 51.3 ? O2 UDP 501 A 1 HETATM 8 O O4 UDP . . . C 2 -52.218 143.212 11.878 1 53.79 ? O4 UDP 501 A 1 HETATM 9 C C1' UDP . . . C 2 -47.882 139.811 12.331 1 46.51 ? C1' UDP 501 A 1 HETATM 10 C C2' UDP . . . C 2 -46.995 140.059 13.283 1 50.4 ? C2' UDP 501 A 1 HETATM 11 O O2' UDP . . . C 2 -46.152 141.225 12.969 1 53.22 ? O2' UDP 501 A 1 HETATM 12 C C3' UDP . . . C 2 -46.171 138.751 13.245 1 45.96 ? C3' UDP 501 A 1 HETATM 13 C C4' UDP . . . C 2 -47.235 137.647 12.849 1 47.28 ? C4' UDP 501 A 1 HETATM 14 O O4' UDP . . . C 2 -48.351 138.295 12.684 1 47.24 ? O4' UDP 501 A 1 HETATM 15 O O3' UDP . . . C 2 -45.223 138.812 12.318 1 49.92 ? O3' UDP 501 A 1 HETATM 16 C C5' UDP . . . C 2 -47.356 136.63 13.964 1 48.14 ? C5' UDP 501 A 1 HETATM 17 O O5' UDP . . . C 2 -46.365 135.651 13.791 1 42.94 ? O5' UDP 501 A 1 HETATM 18 P PA UDP . . . C 2 -46.058 134.687 15 1 49.64 ? PA UDP 501 A 1 HETATM 19 O O1A UDP . . . C 2 -44.886 133.795 14.657 1 46.11 -1 O1A UDP 501 A 1 HETATM 20 O O2A UDP . . . C 2 -45.728 135.501 16.229 1 47.52 ? O2A UDP 501 A 1 HETATM 21 O O3A UDP . . . C 2 -47.334 133.806 15.327 1 47.38 ? O3A UDP 501 A 1 HETATM 22 P PB UDP . . . C 2 -48.273 133.116 14.265 1 44.8 ? PB UDP 501 A 1 HETATM 23 O O1B UDP . . . C 2 -47.452 132.609 13.099 1 48.16 -1 O1B UDP 501 A 1 HETATM 24 O O2B UDP . . . C 2 -49.282 134.111 13.76 1 46.93 -1 O2B UDP 501 A 1 HETATM 25 O O3B UDP . . . C 2 -49.002 131.963 14.911 1 41.65 ? O3B UDP 501 A 1 HETATM 26 H HN3 UDP . . . C 2 -51.629 141.341 10.34 1 59.47 ? HN3 UDP 501 A 1 HETATM 27 H H5 UDP . . . C 2 -50.47 143.332 13.769 1 53.63 ? H5 UDP 501 A 1 HETATM 28 H H6 UDP . . . C 2 -48.55 141.829 13.977 1 61.32 ? H6 UDP 501 A 1 HETATM 29 H H1' UDP . . . C 2 -47.427 139.811 11.464 1 55.81 ? H1' UDP 501 A 1 HETATM 30 H H2' UDP . . . C 2 -47.435 140.168 14.15 1 60.48 ? H2' UDP 501 A 1 HETATM 31 H HO2' UDP . . . C 2 -45.616 141.028 12.287 1 63.86 ? HO2' UDP 501 A 1 HETATM 32 H H3' UDP . . . C 2 -45.786 138.56 14.123 1 55.15 ? H3' UDP 501 A 1 HETATM 33 H H4' UDP . . . C 2 -46.972 137.207 12.016 1 56.73 ? H4' UDP 501 A 1 HETATM 34 H HO3' UDP . . . C 2 -44.591 139.385 12.576 1 59.91 ? HO3' UDP 501 A 1 HETATM 35 H "H5'1" UDP . . . C 2 -48.241 136.213 13.938 1 57.77 ? "H5'1" UDP 501 A 1 HETATM 36 H "H5'2" UDP . . . C 2 -47.227 137.076 14.826 1 57.77 ? "H5'2" UDP 501 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 36 #