data_5HUU # _model_server_result.job_id EI9bpHV8YfhRU0jXFct-bA _model_server_result.datetime_utc '2024-11-05 00:28:46' _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":"E","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 . . . E 2 -69.502 100.654 40.391 1 55.04 ? N1 UDP 501 B 1 HETATM 2 C C2 UDP . . . E 2 -69.923 101.542 41.474 1 50.48 ? C2 UDP 501 B 1 HETATM 3 N N3 UDP . . . E 2 -71.309 101.987 41.577 1 52.7 ? N3 UDP 501 B 1 HETATM 4 C C4 UDP . . . E 2 -72.266 101.553 40.628 1 56.58 ? C4 UDP 501 B 1 HETATM 5 C C5 UDP . . . E 2 -71.857 100.656 39.539 1 51.02 ? C5 UDP 501 B 1 HETATM 6 C C6 UDP . . . E 2 -70.46 100.209 39.439 1 48.32 ? C6 UDP 501 B 1 HETATM 7 O O2 UDP . . . E 2 -69.113 101.921 42.292 1 60.98 ? O2 UDP 501 B 1 HETATM 8 O O4 UDP . . . E 2 -73.423 101.925 40.721 1 57.85 ? O4 UDP 501 B 1 HETATM 9 C C1' UDP . . . E 2 -68.166 100.251 40.363 1 48.28 ? C1' UDP 501 B 1 HETATM 10 C C2' UDP . . . E 2 -67.842 99.467 39.347 1 53.35 ? C2' UDP 501 B 1 HETATM 11 O O2' UDP . . . E 2 -68.342 98.092 39.517 1 55.74 ? O2' UDP 501 B 1 HETATM 12 C C3' UDP . . . E 2 -66.305 99.506 39.455 1 58.15 ? C3' UDP 501 B 1 HETATM 13 C C4' UDP . . . E 2 -66.015 101.005 39.871 1 58.03 ? C4' UDP 501 B 1 HETATM 14 O O4' UDP . . . E 2 -67.166 101.521 40.195 1 49.36 ? O4' UDP 501 B 1 HETATM 15 O O3' UDP . . . E 2 -65.859 98.681 40.399 1 55.68 ? O3' UDP 501 B 1 HETATM 16 C C5' UDP . . . E 2 -65.392 101.715 38.687 1 51.95 ? C5' UDP 501 B 1 HETATM 17 O O5' UDP . . . E 2 -64.002 101.524 38.786 1 52.52 ? O5' UDP 501 B 1 HETATM 18 P PA UDP . . . E 2 -63.079 101.858 37.56 1 56.5 ? PA UDP 501 B 1 HETATM 19 O O1A UDP . . . E 2 -63.502 101.009 36.382 1 53.54 -1 O1A UDP 501 B 1 HETATM 20 O O2A UDP . . . E 2 -61.651 101.556 37.947 1 58.17 ? O2A UDP 501 B 1 HETATM 21 O O3A UDP . . . E 2 -63.206 103.393 37.203 1 50.42 ? O3A UDP 501 B 1 HETATM 22 P PB UDP . . . E 2 -63.251 104.547 38.283 1 54.25 ? PB UDP 501 B 1 HETATM 23 O O1B UDP . . . E 2 -62.586 105.789 37.738 1 54.31 -1 O1B UDP 501 B 1 HETATM 24 O O2B UDP . . . E 2 -62.51 104.078 39.512 1 53.68 ? O2B UDP 501 B 1 HETATM 25 O O3B UDP . . . E 2 -64.692 104.858 38.629 1 54.64 -1 O3B UDP 501 B 1 HETATM 26 H HN3 UDP . . . E 2 -71.558 102.545 42.254 1 63.25 ? HN3 UDP 501 B 1 HETATM 27 H H5 UDP . . . E 2 -72.514 100.353 38.883 1 61.22 ? H5 UDP 501 B 1 HETATM 28 H H6 UDP . . . E 2 -70.189 99.61 38.717 1 57.99 ? H6 UDP 501 B 1 HETATM 29 H H1' UDP . . . E 2 -67.957 99.789 41.2 1 57.94 ? H1' UDP 501 B 1 HETATM 30 H H2' UDP . . . E 2 -68.144 99.85 38.499 1 64.02 ? H2' UDP 501 B 1 HETATM 31 H HO2' UDP . . . E 2 -67.667 97.556 39.734 1 66.89 ? HO2' UDP 501 B 1 HETATM 32 H H3' UDP . . . E 2 -65.892 99.301 38.592 1 69.78 ? H3' UDP 501 B 1 HETATM 33 H H4' UDP . . . E 2 -65.407 101.03 40.637 1 69.64 ? H4' UDP 501 B 1 HETATM 34 H HO3' UDP . . . E 2 -65.906 99.085 41.192 1 66.81 ? HO3' UDP 501 B 1 HETATM 35 H "H5'1" UDP . . . E 2 -65.726 101.328 37.852 1 62.34 ? "H5'1" UDP 501 B 1 HETATM 36 H "H5'2" UDP . . . E 2 -65.602 102.67 38.726 1 62.34 ? "H5'2" UDP 501 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 237 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 36 #