data_1TWF # _model_server_result.job_id LsDLS_bnXboEJ4LVQVjwEQ _model_server_result.datetime_utc '2025-02-28 08:22:27' _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 1twf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":3571}' # _entry.id 1TWF # _exptl.entry_id 1TWF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 484.141 _entity.id 13 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE 5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _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 1TWF _cell.length_a 123 _cell.length_b 223 _cell.length_c 374 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1TWF _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 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 PQS decameric 10 author_and_software_defined_assembly 1 PISA eicosameric 20 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,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U 1 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U 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' 2_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 123 0 0 # _struct_asym.details ? _struct_asym.entity_id 13 _struct_asym.id P _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A SG CYS 67 A CYS 67 1_555 L ZN ZN . A ZN 3008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.787 ? metalc ? metalc2 A SG CYS 70 A CYS 70 1_555 L ZN ZN . A ZN 3008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.673 ? metalc ? metalc3 A SG CYS 77 A CYS 77 1_555 L ZN ZN . A ZN 3008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.584 ? metalc ? metalc4 A NE2 HIS 80 A HIS 80 1_555 L ZN ZN . A ZN 3008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.61 ? metalc ? metalc5 A SG CYS 107 A CYS 107 1_555 K ZN ZN . A ZN 3006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.5 ? metalc ? metalc6 A SG CYS 110 A CYS 110 1_555 K ZN ZN . A ZN 3006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? metalc ? metalc7 A SG CYS 148 A CYS 148 1_555 K ZN ZN . A ZN 3006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.546 ? metalc ? metalc8 A SG CYS 167 A CYS 167 1_555 K ZN ZN . A ZN 3006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.558 ? metalc ? metalc9 A OD1 ASP 481 A ASP 481 1_555 M MN MN . A MN 3009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? metalc ? metalc10 A OD2 ASP 481 A ASP 481 1_555 N MN MN . A MN 3010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc11 A OD2 ASP 483 A ASP 483 1_555 M MN MN . A MN 3009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc12 A OD1 ASP 483 A ASP 483 1_555 N MN MN . A MN 3010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc13 A OD2 ASP 485 A ASP 485 1_555 M MN MN . A MN 3009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.294 ? metalc ? metalc14 M MN MN . A MN 3009 1_555 P O1B UTP . B UTP 3571 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.733 ? metalc ? metalc15 M MN MN . A MN 3009 1_555 P O2G UTP . B UTP 3571 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.477 ? metalc ? metalc16 N MN MN . A MN 3010 1_555 B OD2 ASP 837 B ASP 837 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.663 ? metalc ? metalc17 N MN MN . A MN 3010 1_555 P O1B UTP . B UTP 3571 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.552 ? metalc ? metalc18 B SG CYS 1163 B CYS 1163 1_555 O ZN ZN . B ZN 3007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.757 ? metalc ? metalc19 B SG CYS 1166 B CYS 1166 1_555 O ZN ZN . B ZN 3007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.591 ? metalc ? metalc20 B SG CYS 1182 B CYS 1182 1_555 O ZN ZN . B ZN 3007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.754 ? metalc ? metalc21 B SG CYS 1185 B CYS 1185 1_555 O ZN ZN . B ZN 3007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.716 ? metalc ? metalc22 C SG CYS 86 C CYS 86 1_555 Q ZN ZN . C ZN 3002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc23 C SG CYS 88 C CYS 88 1_555 Q ZN ZN . C ZN 3002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc24 C SG CYS 92 C CYS 92 1_555 Q ZN ZN . C ZN 3002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.676 ? metalc ? metalc25 C SG CYS 95 C CYS 95 1_555 Q ZN ZN . C ZN 3002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? metalc ? metalc26 G SG CYS 7 I CYS 7 1_555 R ZN ZN . I ZN 3003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.545 ? metalc ? metalc27 G SG CYS 10 I CYS 10 1_555 R ZN ZN . I ZN 3003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc28 G SG CYS 29 I CYS 29 1_555 R ZN ZN . I ZN 3003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.521 ? metalc ? metalc29 G SG CYS 32 I CYS 32 1_555 R ZN ZN . I ZN 3003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? metalc ? metalc30 G SG CYS 75 I CYS 75 1_555 S ZN ZN . I ZN 3004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? metalc ? metalc31 G SG CYS 78 I CYS 78 1_555 S ZN ZN . I ZN 3004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.58 ? metalc ? metalc32 G SG CYS 103 I CYS 103 1_555 S ZN ZN . I ZN 3004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.664 ? metalc ? metalc33 G SG CYS 106 I CYS 106 1_555 S ZN ZN . I ZN 3004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc34 H SG CYS 7 J CYS 7 1_555 T ZN ZN . J ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.386 ? metalc ? metalc35 H SG CYS 10 J CYS 10 1_555 T ZN ZN . J ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.325 ? metalc ? metalc36 H SG CYS 45 J CYS 45 1_555 T ZN ZN . J ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? metalc ? metalc37 H SG CYS 46 J CYS 46 1_555 T ZN ZN . J ZN 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? metalc ? metalc38 J SG CYS 31 L CYS 31 1_555 U ZN ZN . L ZN 3005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.753 ? metalc ? metalc39 J SG CYS 34 L CYS 34 1_555 U ZN ZN . L ZN 3005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.565 ? metalc ? metalc40 J SG CYS 48 L CYS 48 1_555 U ZN ZN . L ZN 3005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.769 ? # _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 356 n n PA O2A UTP sing 357 n n PA O3A UTP sing 358 n n PA O5' UTP sing 359 n n O2A H2A UTP sing 360 n n O3A PB UTP sing 361 n n O5' C5' UTP sing 362 n n PB O1B UTP sing 363 n n PB O2B UTP doub 364 n n PB O3B UTP sing 365 n n O1B H1B UTP sing 366 n n O3B PG UTP sing 367 n n PG O1G UTP sing 368 n n PG O2G UTP doub 369 n n PG O3G UTP sing 370 n n O1G H1G UTP sing 371 n n O3G H3G UTP sing 372 n n C5' C4' UTP sing 373 n n C5' "H5'1" UTP sing 374 n n C5' "H5'2" UTP sing 375 n n C4' O4' UTP sing 376 n n C4' C3' UTP sing 377 n n C4' H4' UTP sing 378 n n O4' C1' UTP sing 379 n n C1' C2' UTP sing 380 n n C1' N1 UTP sing 381 n n C1' H1' UTP sing 382 n n C2' O2' UTP sing 383 n n C2' C3' UTP sing 384 n n C2' H2' UTP sing 385 n n O2' HA UTP sing 386 n n C3' O3' UTP sing 387 n n C3' H3' UTP sing 388 n n O3' HB UTP sing 389 n n N1 C6 UTP sing 390 n y N1 C2 UTP sing 391 n y C6 C5 UTP doub 392 n y C6 H6 UTP sing 393 n n C2 O2 UTP doub 394 n n C2 N3 UTP sing 395 n y N3 C4 UTP sing 396 n y N3 H3 UTP sing 397 n n C4 O4 UTP doub 398 n n C4 C5 UTP sing 399 n y C5 H5 UTP sing 400 n n # _atom_sites.entry_id 1TWF _atom_sites.fract_transf_matrix[1][1] 0.00813 _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] 0.004484 _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] 0.002674 _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 K 11 ZN A 1 3006 3006 ZN ZN . L 11 ZN A 1 3008 3008 ZN ZN . M 12 MN A 1 3009 3009 MN MN . N 12 MN A 1 3010 3010 MN MN . O 11 ZN B 1 3007 3007 ZN ZN . P 13 UTP B 1 3571 3571 UTP UTP . Q 11 ZN C 1 3002 3002 ZN ZN . R 11 ZN I 1 3003 3003 ZN ZN . S 11 ZN I 1 3004 3004 ZN ZN . T 11 ZN J 1 3001 3001 ZN ZN . U 11 ZN L 1 3005 3005 ZN ZN . # 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 . . . P 13 88.589 43.24 41.982 1 62.39 ? PA UTP 3571 B 1 HETATM 2 O O1A UTP . . . P 13 89.108 43.6 40.632 1 57.59 ? O1A UTP 3571 B 1 HETATM 3 O O2A UTP . . . P 13 88.501 41.779 42.392 1 63.86 ? O2A UTP 3571 B 1 HETATM 4 O O3A UTP . . . P 13 87.115 43.901 42.24 1 61.3 ? O3A UTP 3571 B 1 HETATM 5 O O5' UTP . . . P 13 89.319 44.069 43.109 1 60.98 ? O5' UTP 3571 B 1 HETATM 6 P PB UTP . . . P 13 85.912 44.249 41.275 1 62.76 ? PB UTP 3571 B 1 HETATM 7 O O1B UTP . . . P 13 86.183 44.13 39.855 1 59.97 ? O1B UTP 3571 B 1 HETATM 8 O O2B UTP . . . P 13 85.46 45.556 41.761 1 54.79 ? O2B UTP 3571 B 1 HETATM 9 O O3B UTP . . . P 13 84.974 43.038 41.683 1 59.94 ? O3B UTP 3571 B 1 HETATM 10 P PG UTP . . . P 13 83.527 42.601 41.179 1 64.87 ? PG UTP 3571 B 1 HETATM 11 O O1G UTP . . . P 13 82.639 42.513 42.459 1 57.64 ? O1G UTP 3571 B 1 HETATM 12 O O2G UTP . . . P 13 83.094 43.688 40.185 1 53.28 ? O2G UTP 3571 B 1 HETATM 13 O O3G UTP . . . P 13 83.678 41.216 40.503 1 60.59 ? O3G UTP 3571 B 1 HETATM 14 C C5' UTP . . . P 13 88.967 43.858 44.452 1 60.49 ? C5' UTP 3571 B 1 HETATM 15 C C4' UTP . . . P 13 89.482 44.997 45.276 1 60.8 ? C4' UTP 3571 B 1 HETATM 16 O O4' UTP . . . P 13 89.233 46.272 44.609 1 62.95 ? O4' UTP 3571 B 1 HETATM 17 C C1' UTP . . . P 13 89.163 47.21 45.63 1 63.72 ? C1' UTP 3571 B 1 HETATM 18 C C2' UTP . . . P 13 88.217 46.493 46.613 1 63.45 ? C2' UTP 3571 B 1 HETATM 19 O O2' UTP . . . P 13 88.076 47.15 47.857 1 60.99 ? O2' UTP 3571 B 1 HETATM 20 C C3' UTP . . . P 13 88.839 45.073 46.649 1 61.82 ? C3' UTP 3571 B 1 HETATM 21 O O3' UTP . . . P 13 89.865 44.903 47.657 1 59.27 ? O3' UTP 3571 B 1 HETATM 22 N N1 UTP . . . P 13 88.647 48.568 45.131 1 64.66 ? N1 UTP 3571 B 1 HETATM 23 C C6 UTP . . . P 13 87.888 48.715 43.973 1 63.97 ? C6 UTP 3571 B 1 HETATM 24 C C2 UTP . . . P 13 88.983 49.723 45.916 1 65.69 ? C2 UTP 3571 B 1 HETATM 25 O O2 UTP . . . P 13 89.666 49.644 46.953 1 65.54 ? O2 UTP 3571 B 1 HETATM 26 N N3 UTP . . . P 13 88.51 50.929 45.418 1 64.75 ? N3 UTP 3571 B 1 HETATM 27 C C4 UTP . . . P 13 87.741 51.13 44.263 1 63.36 ? C4 UTP 3571 B 1 HETATM 28 O O4 UTP . . . P 13 87.403 52.303 43.956 1 63.7 ? O4 UTP 3571 B 1 HETATM 29 C C5 UTP . . . P 13 87.445 49.921 43.518 1 64.7 ? C5 UTP 3571 B 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 59 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 29 #