data_7Q13 # _model_server_result.job_id 40x40tMn6kO1srEqwkaZTg _model_server_result.datetime_utc '2025-04-26 01:20:57' _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 7q13 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":802}' # _entry.id 7Q13 # _exptl.entry_id 7Q13 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 404.161 _entity.id 4 _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 7Q13 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7Q13 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _pdbx_struct_assembly.details author_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,S,T _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 ? _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 ? 4 J N N ? 4 M N N ? 4 P N N ? 4 S 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 409 n n N1 C6 UDP sing 410 n n N1 C1' UDP sing 411 n n C2 N3 UDP sing 412 n n C2 O2 UDP doub 413 n n N3 C4 UDP sing 414 n n N3 HN3 UDP sing 415 n n C4 C5 UDP sing 416 n n C4 O4 UDP doub 417 n n C5 C6 UDP doub 418 n n C5 H5 UDP sing 419 n n C6 H6 UDP sing 420 n n C1' C2' UDP sing 421 n n C1' O4' UDP sing 422 n n C1' H1' UDP sing 423 n n C2' O2' UDP sing 424 n n C2' C3' UDP sing 425 n n C2' H2' UDP sing 426 n n O2' HO2' UDP sing 427 n n C3' C4' UDP sing 428 n n C3' O3' UDP sing 429 n n C3' H3' UDP sing 430 n n C4' O4' UDP sing 431 n n C4' C5' UDP sing 432 n n C4' H4' UDP sing 433 n n O3' HO3' UDP sing 434 n n C5' O5' UDP sing 435 n n C5' "H5'1" UDP sing 436 n n C5' "H5'2" UDP sing 437 n n O5' PA UDP sing 438 n n PA O1A UDP doub 439 n n PA O2A UDP sing 440 n n PA O3A UDP sing 441 n n O2A HOA2 UDP sing 442 n n O3A PB UDP sing 443 n n PB O1B UDP doub 444 n n PB O2B UDP sing 445 n n PB O3B UDP sing 446 n n O2B HOB2 UDP sing 447 n n O3B HOB3 UDP sing 448 n n # _atom_sites.entry_id 7Q13 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 I 3 G6P A 1 801 701 G6P G6P . J 4 UDP A 1 802 702 UDP UDP . K 5 GLC A 1 803 703 GLC GLC . L 3 G6P B 1 801 701 G6P G6P . M 4 UDP B 1 802 702 UDP UDP . N 5 GLC B 1 803 703 GLC GLC . O 3 G6P C 1 801 701 G6P G6P . P 4 UDP C 1 802 702 UDP UDP . Q 5 GLC C 1 803 703 GLC GLC . R 3 G6P D 1 801 701 G6P G6P . S 4 UDP D 1 802 702 UDP UDP . T 5 GLC D 1 803 703 GLC GLC . # 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 . . . J 4 147.395 193.386 157.015 1 29.04 ? N1 UDP 802 A 1 HETATM 2 C C2 UDP . . . J 4 148.637 192.758 156.811 1 29.04 ? C2 UDP 802 A 1 HETATM 3 N N3 UDP . . . J 4 149.596 192.845 157.727 1 29.04 ? N3 UDP 802 A 1 HETATM 4 C C4 UDP . . . J 4 149.387 193.524 158.853 1 29.04 ? C4 UDP 802 A 1 HETATM 5 C C5 UDP . . . J 4 148.172 194.161 159.086 1 29.04 ? C5 UDP 802 A 1 HETATM 6 C C6 UDP . . . J 4 147.167 194.075 158.136 1 29.04 ? C6 UDP 802 A 1 HETATM 7 O O2 UDP . . . J 4 148.851 192.111 155.768 1 29.04 ? O2 UDP 802 A 1 HETATM 8 O O4 UDP . . . J 4 150.307 193.582 159.691 1 29.04 ? O4 UDP 802 A 1 HETATM 9 C C1' UDP . . . J 4 146.361 193.271 155.991 1 29.04 ? C1' UDP 802 A 1 HETATM 10 C C2' UDP . . . J 4 145.404 192.149 156.35 1 29.04 ? C2' UDP 802 A 1 HETATM 11 O O2' UDP . . . J 4 145.706 190.966 155.608 1 29.04 ? O2' UDP 802 A 1 HETATM 12 C C3' UDP . . . J 4 144.029 192.656 155.986 1 29.04 ? C3' UDP 802 A 1 HETATM 13 C C4' UDP . . . J 4 144.223 194.109 155.612 1 29.04 ? C4' UDP 802 A 1 HETATM 14 O O4' UDP . . . J 4 145.573 194.457 155.922 1 29.04 ? O4' UDP 802 A 1 HETATM 15 O O3' UDP . . . J 4 143.515 191.919 154.878 1 29.04 ? O3' UDP 802 A 1 HETATM 16 C C5' UDP . . . J 4 143.27 194.991 156.386 1 29.04 ? C5' UDP 802 A 1 HETATM 17 O O5' UDP . . . J 4 142.212 195.359 155.514 1 29.04 ? O5' UDP 802 A 1 HETATM 18 P PA UDP . . . J 4 140.899 196.067 156.103 1 29.04 ? PA UDP 802 A 1 HETATM 19 O O1A UDP . . . J 4 139.786 195.876 155.107 1 29.04 ? O1A UDP 802 A 1 HETATM 20 O O2A UDP . . . J 4 140.71 195.558 157.512 1 29.04 ? O2A UDP 802 A 1 HETATM 21 O O3A UDP . . . J 4 141.266 197.636 156.185 1 29.04 ? O3A UDP 802 A 1 HETATM 22 P PB UDP . . . J 4 142.243 198.419 155.166 1 29.04 ? PB UDP 802 A 1 HETATM 23 O O1B UDP . . . J 4 142.084 197.751 153.822 1 29.04 ? O1B UDP 802 A 1 HETATM 24 O O2B UDP . . . J 4 143.609 198.275 155.786 1 29.04 ? O2B UDP 802 A 1 HETATM 25 O O3B UDP . . . J 4 141.71 199.828 155.207 1 29.04 ? O3B UDP 802 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 32 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 346 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #