data_7BIX # _model_server_result.job_id tN74mQkFs-6FYzJHZfclbw _model_server_result.datetime_utc '2024-10-12 01:24:40' _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 7bix # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"V","auth_seq_id":301}' # _entry.id 7BIX # _exptl.entry_id 7BIX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 484.141 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE 5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 121.39 _cell.angle_gamma 90 _cell.entry_id 7BIX _cell.length_a 197.47 _cell.length_b 152.82 _cell.length_c 125.11 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7BIX _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # 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,AA,BA,CA,DA,EA,FA 1 1 G,H,I,J,K,L,T,U,V,W,X,Y,Z,GA,HA,IA,JA,KA,LA 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 O N N ? 2 Q N N ? 2 T N N ? 2 V N N ? 2 X N N # _chem_comp.formula 'C9 H15 N2 O15 P3' _chem_comp.formula_weight 484.141 _chem_comp.id UTP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE 5'-TRIPHOSPHATE" _chem_comp.type non-polymer _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 PA O1A UTP doub 370 n n PA O2A UTP sing 371 n n PA O3A UTP sing 372 n n PA O5' UTP sing 373 n n O2A H2A UTP sing 374 n n O3A PB UTP sing 375 n n O5' C5' UTP sing 376 n n PB O1B UTP sing 377 n n PB O2B UTP doub 378 n n PB O3B UTP sing 379 n n O1B H1B UTP sing 380 n n O3B PG UTP sing 381 n n PG O1G UTP sing 382 n n PG O2G UTP doub 383 n n PG O3G UTP sing 384 n n O1G H1G UTP sing 385 n n O3G H3G UTP sing 386 n n C5' C4' UTP sing 387 n n C5' "H5'1" UTP sing 388 n n C5' "H5'2" UTP sing 389 n n C4' O4' UTP sing 390 n n C4' C3' UTP sing 391 n n C4' H4' UTP sing 392 n n O4' C1' UTP sing 393 n n C1' C2' UTP sing 394 n n C1' N1 UTP sing 395 n n C1' H1' UTP sing 396 n n C2' O2' UTP sing 397 n n C2' C3' UTP sing 398 n n C2' H2' UTP sing 399 n n O2' HA UTP sing 400 n n C3' O3' UTP sing 401 n n C3' H3' UTP sing 402 n n O3' HB UTP sing 403 n n N1 C6 UTP sing 404 n y N1 C2 UTP sing 405 n y C6 C5 UTP doub 406 n y C6 H6 UTP sing 407 n n C2 O2 UTP doub 408 n n C2 N3 UTP sing 409 n y N3 C4 UTP sing 410 n y N3 H3 UTP sing 411 n n C4 O4 UTP doub 412 n n C4 C5 UTP sing 413 n y C5 H5 UTP sing 414 n n # _atom_sites.entry_id 7BIX _atom_sites.fract_transf_matrix[1][1] 0.005064 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00309 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006544 _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] 0.009363 _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 UTP A 1 301 1 UTP UTP . N 3 UDP B 1 300 300 UDP UDP . O 2 UTP C 1 301 2 UTP UTP . P 3 UDP C 1 302 300 UDP UDP . Q 2 UTP D 1 301 5 UTP UTP . R 3 UDP D 1 302 263 UDP UDP . S 3 UDP E 1 301 263 UDP UDP . T 2 UTP G 1 301 4 UTP UTP . U 3 UDP H 1 301 263 UDP UDP . V 2 UTP I 1 301 3 UTP UTP . W 3 UDP I 1 302 263 UDP UDP . X 2 UTP J 1 301 6 UTP UTP . Y 3 UDP J 1 302 263 UDP UDP . Z 3 UDP K 1 301 263 UDP UDP . AA 4 HOH A 1 401 26 HOH HOH . AA 4 HOH A 2 402 22 HOH HOH . AA 4 HOH A 3 403 21 HOH HOH . BA 4 HOH B 1 401 25 HOH HOH . BA 4 HOH B 2 402 23 HOH HOH . CA 4 HOH C 1 401 31 HOH HOH . CA 4 HOH C 2 402 32 HOH HOH . CA 4 HOH C 3 403 7 HOH HOH . CA 4 HOH C 4 404 34 HOH HOH . DA 4 HOH D 1 401 15 HOH HOH . DA 4 HOH D 2 402 24 HOH HOH . DA 4 HOH D 3 403 38 HOH HOH . DA 4 HOH D 4 404 20 HOH HOH . DA 4 HOH D 5 405 37 HOH HOH . EA 4 HOH E 1 401 6 HOH HOH . EA 4 HOH E 2 402 33 HOH HOH . EA 4 HOH E 3 403 5 HOH HOH . EA 4 HOH E 4 404 36 HOH HOH . EA 4 HOH E 5 405 27 HOH HOH . FA 4 HOH F 1 301 17 HOH HOH . FA 4 HOH F 2 302 19 HOH HOH . FA 4 HOH F 3 303 18 HOH HOH . FA 4 HOH F 4 304 16 HOH HOH . FA 4 HOH F 5 305 28 HOH HOH . FA 4 HOH F 6 306 35 HOH HOH . GA 4 HOH G 1 401 44 HOH HOH . GA 4 HOH G 2 402 2 HOH HOH . GA 4 HOH G 3 403 1 HOH HOH . GA 4 HOH G 4 404 30 HOH HOH . GA 4 HOH G 5 405 3 HOH HOH . GA 4 HOH G 6 406 4 HOH HOH . HA 4 HOH H 1 401 29 HOH HOH . IA 4 HOH I 1 401 46 HOH HOH . IA 4 HOH I 2 402 8 HOH HOH . IA 4 HOH I 3 403 45 HOH HOH . IA 4 HOH I 4 404 39 HOH HOH . IA 4 HOH I 5 405 40 HOH HOH . JA 4 HOH J 1 401 4 HOH HOH . JA 4 HOH J 2 402 13 HOH HOH . JA 4 HOH J 3 403 9 HOH HOH . JA 4 HOH J 4 404 42 HOH HOH . JA 4 HOH J 5 405 43 HOH HOH . JA 4 HOH J 6 406 14 HOH HOH . JA 4 HOH J 7 407 41 HOH HOH . JA 4 HOH J 8 408 2 HOH HOH . KA 4 HOH K 1 401 47 HOH HOH . KA 4 HOH K 2 402 1 HOH HOH . KA 4 HOH K 3 403 3 HOH HOH . KA 4 HOH K 4 404 12 HOH HOH . LA 4 HOH L 1 301 8 HOH HOH . LA 4 HOH L 2 302 5 HOH HOH . LA 4 HOH L 3 303 7 HOH HOH . LA 4 HOH L 4 304 6 HOH HOH . LA 4 HOH L 5 305 10 HOH HOH . LA 4 HOH L 6 306 11 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 P PA UTP . . . V 2 -15.921 20.369 9.003 1 71.82 ? PA UTP 301 I 1 HETATM 2 O O1A UTP . . . V 2 -16.902 21.373 9.081 1 71.82 ? O1A UTP 301 I 1 HETATM 3 O O2A UTP . . . V 2 -14.79 21.131 9.37 1 73.45 ? O2A UTP 301 I 1 HETATM 4 O O3A UTP . . . V 2 -15.746 19.755 7.53 1 75.8 ? O3A UTP 301 I 1 HETATM 5 O O5' UTP . . . V 2 -16.19 19.186 10.039 1 68.39 ? O5' UTP 301 I 1 HETATM 6 P PB UTP . . . V 2 -16.846 19.527 6.372 1 79.82 ? PB UTP 301 I 1 HETATM 7 O O1B UTP . . . V 2 -18.037 20.229 6.651 1 80.74 ? O1B UTP 301 I 1 HETATM 8 O O2B UTP . . . V 2 -17.33 18.188 6.308 1 80.26 ? O2B UTP 301 I 1 HETATM 9 O O3B UTP . . . V 2 -16.225 19.846 4.943 1 77.33 ? O3B UTP 301 I 1 HETATM 10 P PG UTP . . . V 2 -16.683 21.034 3.996 1 77.86 ? PG UTP 301 I 1 HETATM 11 O O1G UTP . . . V 2 -17.533 21.996 4.581 1 82.48 ? O1G UTP 301 I 1 HETATM 12 O O2G UTP . . . V 2 -17.317 20.65 2.79 1 82.98 -1 O2G UTP 301 I 1 HETATM 13 O O3G UTP . . . V 2 -15.626 21.812 3.473 1 76.8 ? O3G UTP 301 I 1 HETATM 14 C C5' UTP . . . V 2 -15.329 18.117 10.019 1 61.47 ? C5' UTP 301 I 1 HETATM 15 C C4' UTP . . . V 2 -15.857 17.16 11.006 1 56.49 ? C4' UTP 301 I 1 HETATM 16 O O4' UTP . . . V 2 -15.901 17.813 12.27 1 56.52 ? O4' UTP 301 I 1 HETATM 17 C C1' UTP . . . V 2 -17.123 17.485 12.951 1 53.38 ? C1' UTP 301 I 1 HETATM 18 C C2' UTP . . . V 2 -18.072 17.228 11.85 1 60.69 ? C2' UTP 301 I 1 HETATM 19 O O2' UTP . . . V 2 -18.978 16.208 12.243 1 68.68 ? O2' UTP 301 I 1 HETATM 20 C C3' UTP . . . V 2 -17.253 16.842 10.682 1 59.8 ? C3' UTP 301 I 1 HETATM 21 O O3' UTP . . . V 2 -17.277 15.459 10.401 1 61.09 ? O3' UTP 301 I 1 HETATM 22 N N1 UTP . . . V 2 -17.435 18.595 13.754 1 47.53 ? N1 UTP 301 I 1 HETATM 23 C C6 UTP . . . V 2 -17.964 19.831 13.206 1 45.7 ? C6 UTP 301 I 1 HETATM 24 C C2 UTP . . . V 2 -17.161 18.528 15.142 1 56.38 ? C2 UTP 301 I 1 HETATM 25 O O2 UTP . . . V 2 -16.715 17.546 15.596 1 70.81 ? O2 UTP 301 I 1 HETATM 26 N N3 UTP . . . V 2 -17.417 19.612 15.985 1 46.56 ? N3 UTP 301 I 1 HETATM 27 C C4 UTP . . . V 2 -17.937 20.778 15.464 1 43.46 ? C4 UTP 301 I 1 HETATM 28 O O4 UTP . . . V 2 -18.17 21.68 16.157 1 49.21 ? O4 UTP 301 I 1 HETATM 29 C C5 UTP . . . V 2 -18.21 20.865 14.003 1 44.58 ? C5 UTP 301 I 1 HETATM 30 H "H5'1" UTP . . . V 2 -15.316 17.715 9.136 1 73.94 ? "H5'1" UTP 301 I 1 HETATM 31 H "H5'2" UTP . . . V 2 -14.436 18.4 10.271 1 73.94 ? "H5'2" UTP 301 I 1 HETATM 32 H H4' UTP . . . V 2 -15.316 16.356 11.047 1 67.97 ? H4' UTP 301 I 1 HETATM 33 H H1' UTP . . . V 2 -17.006 16.688 13.491 1 64.23 ? H1' UTP 301 I 1 HETATM 34 H H2' UTP . . . V 2 -18.56 18.042 11.648 1 73.01 ? H2' UTP 301 I 1 HETATM 35 H HA UTP . . . V 2 -19.7 16.284 11.801 1 82.59 ? HA UTP 301 I 1 HETATM 36 H H3' UTP . . . V 2 -17.533 17.347 9.903 1 71.93 ? H3' UTP 301 I 1 HETATM 37 H HB UTP . . . V 2 -16.498 15.202 10.175 1 73.48 ? HB UTP 301 I 1 HETATM 38 H H6 UTP . . . V 2 -18.14 19.897 12.296 1 55.01 ? H6 UTP 301 I 1 HETATM 39 H H3 UTP . . . V 2 -17.259 19.549 16.828 1 56.05 ? H3 UTP 301 I 1 HETATM 40 H H5 UTP . . . V 2 -18.567 21.646 13.646 1 53.67 ? H5 UTP 301 I 1 # _model_server_stats.io_time_ms 42 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 40 #