data_4KQM # _model_server_result.job_id peYcqt_9a7s7_TUGPL7azA _model_server_result.datetime_utc '2024-10-19 05:27:12' _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 4kqm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":801}' # _entry.id 4KQM # _exptl.entry_id 4KQM _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 4 _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 4KQM _cell.length_a 192.71 _cell.length_b 204.443 _cell.length_c 206.332 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4KQM _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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,M,N,O,P,Q,R _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 ? 2 E N N ? 2 H N N ? 2 M N N ? 2 P 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 449 n n N1 C6 UDP sing 450 n n N1 C1' UDP sing 451 n n C2 N3 UDP sing 452 n n C2 O2 UDP doub 453 n n N3 C4 UDP sing 454 n n N3 HN3 UDP sing 455 n n C4 C5 UDP sing 456 n n C4 O4 UDP doub 457 n n C5 C6 UDP doub 458 n n C5 H5 UDP sing 459 n n C6 H6 UDP sing 460 n n C1' C2' UDP sing 461 n n C1' O4' UDP sing 462 n n C1' H1' UDP sing 463 n n C2' O2' UDP sing 464 n n C2' C3' UDP sing 465 n n C2' H2' UDP sing 466 n n O2' HO2' UDP sing 467 n n C3' C4' UDP sing 468 n n C3' O3' UDP sing 469 n n C3' H3' UDP sing 470 n n C4' O4' UDP sing 471 n n C4' C5' UDP sing 472 n n C4' H4' UDP sing 473 n n O3' HO3' UDP sing 474 n n C5' O5' UDP sing 475 n n C5' "H5'1" UDP sing 476 n n C5' "H5'2" UDP sing 477 n n O5' PA UDP sing 478 n n PA O1A UDP doub 479 n n PA O2A UDP sing 480 n n PA O3A UDP sing 481 n n O2A HOA2 UDP sing 482 n n O3A PB UDP sing 483 n n PB O1B UDP doub 484 n n PB O2B UDP sing 485 n n PB O3B UDP sing 486 n n O2B HOB2 UDP sing 487 n n O3B HOB3 UDP sing 488 n n # _atom_sites.entry_id 4KQM _atom_sites.fract_transf_matrix[1][1] 0.005189 _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] 0.004891 _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] 0.004847 _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 E 2 UDP A 1 801 801 UDP UDP . F 3 G6P A 1 802 901 G6P G6P . G 4 PEG A 1 803 1001 PEG PEG . H 2 UDP B 1 801 801 UDP UDP . I 3 G6P B 1 802 901 G6P G6P . J 4 PEG B 1 803 1001 PEG PEG . K 5 GLC C 1 801 701 GLC GLC . L 6 BGC C 1 802 1101 BGC BGC . M 2 UDP C 1 803 801 UDP UDP . N 3 G6P C 1 804 901 G6P G6P . O 4 PEG C 1 805 1001 PEG PEG . P 2 UDP D 1 801 801 UDP UDP . Q 3 G6P D 1 802 901 G6P G6P . R 4 PEG D 1 803 1001 PEG PEG . # 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 67.901 48.103 125.06 1 54.03 ? N1 UDP 801 A 1 HETATM 2 C C2 UDP . . . E 2 67.723 49.079 124.051 1 52.85 ? C2 UDP 801 A 1 HETATM 3 N N3 UDP . . . E 2 67.603 48.75 122.757 1 51.23 ? N3 UDP 801 A 1 HETATM 4 C C4 UDP . . . E 2 67.657 47.449 122.392 1 50.41 ? C4 UDP 801 A 1 HETATM 5 C C5 UDP . . . E 2 67.833 46.454 123.373 1 47.91 ? C5 UDP 801 A 1 HETATM 6 C C6 UDP . . . E 2 67.961 46.8 124.721 1 49.66 ? C6 UDP 801 A 1 HETATM 7 O O2 UDP . . . E 2 67.669 50.27 124.375 1 57.62 ? O2 UDP 801 A 1 HETATM 8 O O4 UDP . . . E 2 67.55 47.135 121.173 1 47.78 ? O4 UDP 801 A 1 HETATM 9 C C1' UDP . . . E 2 68.036 48.559 126.447 1 55.6 ? C1' UDP 801 A 1 HETATM 10 C C2' UDP . . . E 2 66.966 48.018 127.376 1 59.47 ? C2' UDP 801 A 1 HETATM 11 O O2' UDP . . . E 2 65.987 49.039 127.56 1 60.37 ? O2' UDP 801 A 1 HETATM 12 C C3' UDP . . . E 2 67.696 47.718 128.673 1 60.34 ? C3' UDP 801 A 1 HETATM 13 C C4' UDP . . . E 2 69.183 47.748 128.346 1 58.79 ? C4' UDP 801 A 1 HETATM 14 O O4' UDP . . . E 2 69.3 48.144 126.979 1 59.83 ? O4' UDP 801 A 1 HETATM 15 O O3' UDP . . . E 2 67.431 48.769 129.604 1 59.4 ? O3' UDP 801 A 1 HETATM 16 C C5' UDP . . . E 2 69.853 46.401 128.548 1 59.55 ? C5' UDP 801 A 1 HETATM 17 O O5' UDP . . . E 2 70.741 46.469 129.663 1 65.2 ? O5' UDP 801 A 1 HETATM 18 P PA UDP . . . E 2 71.998 45.464 129.879 1 66.65 ? PA UDP 801 A 1 HETATM 19 O O1A UDP . . . E 2 71.781 44.173 129.117 1 64.18 ? O1A UDP 801 A 1 HETATM 20 O O2A UDP . . . E 2 73.259 46.259 129.604 1 63.87 ? O2A UDP 801 A 1 HETATM 21 O O3A UDP . . . E 2 71.884 45.142 131.451 1 63.12 ? O3A UDP 801 A 1 HETATM 22 P PB UDP . . . E 2 70.597 44.4 132.093 1 72.29 ? PB UDP 801 A 1 HETATM 23 O O1B UDP . . . E 2 70.036 45.453 133.011 1 72.47 ? O1B UDP 801 A 1 HETATM 24 O O2B UDP . . . E 2 71.172 43.212 132.818 1 73.58 ? O2B UDP 801 A 1 HETATM 25 O O3B UDP . . . E 2 69.686 43.985 130.963 1 70.58 ? O3B UDP 801 A 1 # _model_server_stats.io_time_ms 40 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 25 #