data_7BL7 # _model_server_result.job_id bI1ZAR9Lu0cluE-hF0wQ2g _model_server_result.datetime_utc '2024-10-12 01:23:50' _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 7bl7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Y","auth_seq_id":301}' # _entry.id 7BL7 # _exptl.entry_id 7BL7 _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 8 _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 7BL7 _cell.length_a 151.23 _cell.length_b 165.75 _cell.length_c 125.02 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7BL7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall 'P 2 2ab' _symmetry.space_group_name_H-M 'P 21 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA hexameric 6 author_and_software_defined_assembly 1 PISA hexameric 6 author_and_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,B,C,D,E,F,M,N,O,P,Q,R,S,T,CA,DA,EA,FA,GA,HA 1 1 G,H,I,J,K,L,U,V,W,X,Y,Z,AA,BA,IA,JA,KA,LA,MA 2 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 M N N ? 2 P N N ? 2 R N N ? 2 T N N ? 2 V N N ? 2 X N N ? 2 Y N N ? 2 BA 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 330 n n N1 C6 UDP sing 331 n n N1 C1' UDP sing 332 n n C2 N3 UDP sing 333 n n C2 O2 UDP doub 334 n n N3 C4 UDP sing 335 n n N3 HN3 UDP sing 336 n n C4 C5 UDP sing 337 n n C4 O4 UDP doub 338 n n C5 C6 UDP doub 339 n n C5 H5 UDP sing 340 n n C6 H6 UDP sing 341 n n C1' C2' UDP sing 342 n n C1' O4' UDP sing 343 n n C1' H1' UDP sing 344 n n C2' O2' UDP sing 345 n n C2' C3' UDP sing 346 n n C2' H2' UDP sing 347 n n O2' HO2' UDP sing 348 n n C3' C4' UDP sing 349 n n C3' O3' UDP sing 350 n n C3' H3' UDP sing 351 n n C4' O4' UDP sing 352 n n C4' C5' UDP sing 353 n n C4' H4' UDP sing 354 n n O3' HO3' UDP sing 355 n n C5' O5' UDP sing 356 n n C5' "H5'1" UDP sing 357 n n C5' "H5'2" UDP sing 358 n n O5' PA UDP sing 359 n n PA O1A UDP doub 360 n n PA O2A UDP sing 361 n n PA O3A UDP sing 362 n n O2A HOA2 UDP sing 363 n n O3A PB UDP sing 364 n n PB O1B UDP doub 365 n n PB O2B UDP sing 366 n n PB O3B UDP sing 367 n n O2B HOB2 UDP sing 368 n n O3B HOB3 UDP sing 369 n n # _atom_sites.entry_id 7BL7 _atom_sites.fract_transf_matrix[1][1] 0.006612 _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] 0.006033 _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] 0.007999 _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 M 2 UDP B 1 301 5 UDP UDP . N 3 UTP A 1 301 4 UTP UTP . O 3 UTP F 1 301 1 UTP UTP . P 2 UDP E 1 301 6 UDP UDP . Q 3 UTP D 1 301 2 UTP UTP . R 2 UDP D 1 302 2 UDP UDP . S 3 UTP C 1 301 3 UTP UTP . T 2 UDP C 1 302 1 UDP UDP . U 3 UTP I 1 301 2 UTP UTP . V 2 UDP I 1 302 4 UDP UDP . W 3 UTP J 1 301 3 UTP UTP . X 2 UDP J 1 302 3 UDP UDP . Y 2 UDP K 1 301 8 UDP UDP . Z 3 UTP L 1 301 4 UTP UTP . AA 3 UTP G 1 301 1 UTP UTP . BA 2 UDP H 1 301 7 UDP UDP . CA 4 HOH B 1 401 19 HOH HOH . CA 4 HOH B 2 402 1 HOH HOH . CA 4 HOH B 3 403 32 HOH HOH . CA 4 HOH B 4 404 18 HOH HOH . CA 4 HOH B 5 405 24 HOH HOH . CA 4 HOH B 6 406 9 HOH HOH . CA 4 HOH B 7 407 10 HOH HOH . DA 4 HOH A 1 401 22 HOH HOH . EA 4 HOH F 1 401 31 HOH HOH . FA 4 HOH E 1 401 8 HOH HOH . FA 4 HOH E 2 402 21 HOH HOH . FA 4 HOH E 3 403 20 HOH HOH . FA 4 HOH E 4 404 2 HOH HOH . FA 4 HOH E 5 405 36 HOH HOH . FA 4 HOH E 6 406 34 HOH HOH . GA 4 HOH D 1 401 7 HOH HOH . GA 4 HOH D 2 402 41 HOH HOH . GA 4 HOH D 3 403 35 HOH HOH . GA 4 HOH D 4 404 40 HOH HOH . GA 4 HOH D 5 405 30 HOH HOH . GA 4 HOH D 6 406 42 HOH HOH . HA 4 HOH C 1 401 43 HOH HOH . HA 4 HOH C 2 402 6 HOH HOH . HA 4 HOH C 3 403 39 HOH HOH . HA 4 HOH C 4 404 38 HOH HOH . IA 4 HOH I 1 401 33 HOH HOH . IA 4 HOH I 2 402 4 HOH HOH . IA 4 HOH I 3 403 11 HOH HOH . JA 4 HOH J 1 401 16 HOH HOH . JA 4 HOH J 2 402 15 HOH HOH . JA 4 HOH J 3 403 17 HOH HOH . KA 4 HOH L 1 401 37 HOH HOH . LA 4 HOH G 1 401 29 HOH HOH . LA 4 HOH G 2 402 28 HOH HOH . LA 4 HOH G 3 403 27 HOH HOH . LA 4 HOH G 4 404 5 HOH HOH . MA 4 HOH H 1 401 3 HOH HOH . MA 4 HOH H 2 402 23 HOH HOH . MA 4 HOH H 3 403 14 HOH HOH . MA 4 HOH H 4 404 13 HOH HOH . MA 4 HOH H 5 405 12 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 . . . Y 2 31.274 17.59 -1.079 1 36.67 ? N1 UDP 301 K 1 HETATM 2 C C2 UDP . . . Y 2 30.518 17.38 -2.2 1 33.64 ? C2 UDP 301 K 1 HETATM 3 N N3 UDP . . . Y 2 29.66 16.321 -2.133 1 41.48 ? N3 UDP 301 K 1 HETATM 4 C C4 UDP . . . Y 2 29.47 15.491 -1.077 1 35.66 ? C4 UDP 301 K 1 HETATM 5 C C5 UDP . . . Y 2 30.259 15.789 0.066 1 40.14 ? C5 UDP 301 K 1 HETATM 6 C C6 UDP . . . Y 2 31.122 16.814 0.029 1 38.87 ? C6 UDP 301 K 1 HETATM 7 O O2 UDP . . . Y 2 30.574 18.101 -3.166 1 31.6 ? O2 UDP 301 K 1 HETATM 8 O O4 UDP . . . Y 2 28.669 14.571 -1.175 1 23.53 ? O4 UDP 301 K 1 HETATM 9 C C1' UDP . . . Y 2 32.331 18.6 -1.193 1 45.11 ? C1' UDP 301 K 1 HETATM 10 C C2' UDP . . . Y 2 31.864 19.948 -1.689 1 53.46 ? C2' UDP 301 K 1 HETATM 11 O O2' UDP . . . Y 2 33.029 20.604 -2.131 1 56.54 ? O2' UDP 301 K 1 HETATM 12 C C3' UDP . . . Y 2 31.521 20.619 -0.389 1 50.21 ? C3' UDP 301 K 1 HETATM 13 C C4' UDP . . . Y 2 32.701 20.202 0.451 1 27.23 ? C4' UDP 301 K 1 HETATM 14 O O4' UDP . . . Y 2 32.894 18.829 0.08 1 32.26 ? O4' UDP 301 K 1 HETATM 15 O O3' UDP . . . Y 2 31.447 22.02 -0.587 1 55.48 ? O3' UDP 301 K 1 HETATM 16 C C5' UDP . . . Y 2 32.527 20.271 1.938 1 23.19 ? C5' UDP 301 K 1 HETATM 17 O O5' UDP . . . Y 2 31.415 21.104 2.196 1 23.79 ? O5' UDP 301 K 1 HETATM 18 P PA UDP . . . Y 2 30.667 20.929 3.41 1 53.36 ? PA UDP 301 K 1 HETATM 19 O O1A UDP . . . Y 2 29.512 21.73 3.278 1 78.26 ? O1A UDP 301 K 1 HETATM 20 O O2A UDP . . . Y 2 30.377 19.535 3.57 1 72.23 ? O2A UDP 301 K 1 HETATM 21 O O3A UDP . . . Y 2 31.517 21.392 4.659 1 80.27 ? O3A UDP 301 K 1 HETATM 22 P PB UDP . . . Y 2 30.982 22.191 5.908 1 61.58 ? PB UDP 301 K 1 HETATM 23 O O1B UDP . . . Y 2 30.642 23.486 5.582 1 82.67 ? O1B UDP 301 K 1 HETATM 24 O O2B UDP . . . Y 2 29.866 21.409 6.376 1 78.85 ? O2B UDP 301 K 1 HETATM 25 O O3B UDP . . . Y 2 32.054 22.162 6.842 1 79.43 ? O3B UDP 301 K 1 HETATM 26 H HN3 UDP . . . Y 2 29.112 16.146 -2.969 1 49.78 ? HN3 UDP 301 K 1 HETATM 27 H H5 UDP . . . Y 2 30.135 15.165 0.95 1 48.17 ? H5 UDP 301 K 1 HETATM 28 H H6 UDP . . . Y 2 31.738 17.067 0.89 1 46.64 ? H6 UDP 301 K 1 HETATM 29 H H1' UDP . . . Y 2 33.149 18.219 -1.804 1 54.13 ? H1' UDP 301 K 1 HETATM 30 H H2' UDP . . . Y 2 31.069 19.962 -2.433 1 64.15 ? H2' UDP 301 K 1 HETATM 31 H HO2' UDP . . . Y 2 32.898 20.825 -3.091 1 67.85 ? HO2' UDP 301 K 1 HETATM 32 H H3' UDP . . . Y 2 30.579 20.261 0.023 1 60.26 ? H3' UDP 301 K 1 HETATM 33 H H4' UDP . . . Y 2 33.62 20.696 0.138 1 32.68 ? H4' UDP 301 K 1 HETATM 34 H HO3' UDP . . . Y 2 30.586 22.325 -0.199 1 66.57 ? HO3' UDP 301 K 1 HETATM 35 H "H5'1" UDP . . . Y 2 32.385 19.275 2.356 1 27.83 ? "H5'1" UDP 301 K 1 HETATM 36 H "H5'2" UDP . . . Y 2 33.38 20.711 2.451 1 27.83 ? "H5'2" UDP 301 K 1 HETATM 37 H HOA2 UDP . . . Y 2 29.93 19.106 4.346 1 86.67 ? HOA2 UDP 301 K 1 HETATM 38 H HOB2 UDP . . . Y 2 29.608 21.311 7.33 1 94.62 ? HOB2 UDP 301 K 1 HETATM 39 H HOB3 UDP . . . Y 2 32.983 22.466 6.663 1 95.32 ? HOB3 UDP 301 K 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 98 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 39 #