data_3UXP # _model_server_result.job_id vFqgt3LoBiZNlJ4vW9Oitg _model_server_result.datetime_utc '2025-03-05 22:13:37' _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 3uxp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":336}' # _entry.id 3UXP # _exptl.entry_id 3UXP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 466.169 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 102.04 _cell.angle_gamma 90 _cell.entry_id 3UXP _cell.length_a 100.321 _cell.length_b 56.607 _cell.length_c 93.144 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3UXP _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 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,C,D,G,H,I,J,K,P,R,S 1 1 B,E,F,L,M,N,O,Q,T,U 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 ? 4 G N N ? 4 L N 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 O THR 101 A THR 101 1_555 J NA NA . A NA 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc2 A O VAL 103 A VAL 103 1_555 J NA NA . A NA 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc3 A O ILE 106 A ILE 106 1_555 J NA NA . A NA 339 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.358 ? metalc ? metalc4 A OD1 ASP 190 A ASP 190 1_555 I NA NA . A NA 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc5 A O ASP 190 A ASP 190 1_555 I NA NA . A NA 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.647 ? metalc ? metalc6 A OD2 ASP 192 A ASP 192 1_555 I NA NA . A NA 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? metalc ? metalc7 G O1B D3T . A D3T 336 1_555 I NA NA . A NA 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc8 G O1A D3T . A D3T 336 1_555 I NA NA . A NA 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc9 J NA NA . A NA 339 1_555 C OP2 DA 6 P DA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.209 ? metalc ? metalc10 B O THR 101 B THR 101 1_555 N NA NA . B NA 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc11 B O VAL 103 B VAL 103 1_555 N NA NA . B NA 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.568 ? metalc ? metalc12 B O ILE 106 B ILE 106 1_555 N NA NA . B NA 338 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.89 ? metalc ? metalc13 B OD2 ASP 192 B ASP 192 1_555 M NA NA . B NA 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.703 ? metalc ? metalc14 L O1A D3T . B D3T 336 1_555 M NA NA . B NA 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.548 ? metalc ? metalc15 L O1B D3T . B D3T 336 1_555 M NA NA . B NA 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.024 ? metalc ? metalc16 L O3B D3T . B D3T 336 1_555 M NA NA . B NA 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.125 ? metalc ? metalc17 N NA NA . B NA 338 1_555 E OP2 DA 6 D DA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? hydrog WATSON-CRICK hydrog1 C N3 DT 2 P DT 2 1_555 D N1 DA 7 T DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 C O4 DT 2 P DT 2 1_555 D N6 DA 7 T DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 C N1 DG 3 P DG 3 1_555 D N3 DC 6 T DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 C N2 DG 3 P DG 3 1_555 D O2 DC 6 T DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 C O6 DG 3 P DG 3 1_555 D N4 DC 6 T DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 C N3 DT 4 P DT 4 1_555 D N1 DA 5 T DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 C O4 DT 4 P DT 4 1_555 D N6 DA 5 T DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 C N1 DG 5 P DG 5 1_555 D N3 DC 4 T DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 C N2 DG 5 P DG 5 1_555 D O2 DC 4 T DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 C O6 DG 5 P DG 5 1_555 D N4 DC 4 T DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 C N1 DA 6 P DA 6 1_555 D N3 DT 3 T DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 C N6 DA 6 P DA 6 1_555 D O4 DT 3 T DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog13 C N2 DG 7 P DG 7 1_555 D O2 DC 2 T DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 E N3 DT 2 D DT 2 1_555 F N1 DA 7 E DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 E O4 DT 2 D DT 2 1_555 F N6 DA 7 E DA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 E N1 DG 3 D DG 3 1_555 F N3 DC 6 E DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 E N2 DG 3 D DG 3 1_555 F O2 DC 6 E DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 E O6 DG 3 D DG 3 1_555 F N4 DC 6 E DC 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 E N3 DT 4 D DT 4 1_555 F N1 DA 5 E DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 E O4 DT 4 D DT 4 1_555 F N6 DA 5 E DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 E N1 DG 5 D DG 5 1_555 F N3 DC 4 E DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 E N2 DG 5 D DG 5 1_555 F O2 DC 4 E DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 E O6 DG 5 D DG 5 1_555 F N4 DC 4 E DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 E N1 DA 6 D DA 6 1_555 F N3 DT 3 E DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 E N6 DA 6 D DA 6 1_555 F O4 DT 3 E DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DC PAIR' hydrog26 E N1 DG 7 D DG 7 1_555 F N3 DC 2 E DC 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DG-DT MISPAIR' hydrog27 E N2 DG 7 D DG 7 1_555 F O2 DT 3 E DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H17 N2 O13 P3' _chem_comp.formula_weight 466.169 _chem_comp.id D3T _chem_comp.mon_nstd_flag n _chem_comp.name "2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE" _chem_comp.type 'dna oh 3 prime terminus' _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 D3T doub 83 n n PA O2A D3T sing 84 n n PA O5' D3T sing 85 n n PA O3A D3T sing 86 n n O2A HOA2 D3T sing 87 n n O5' C5' D3T sing 88 n n C5' C4' D3T sing 89 n n C5' "H5'1" D3T sing 90 n n C5' "H5'2" D3T sing 91 n n C4' O4' D3T sing 92 n n C4' C3' D3T sing 93 n n C4' H4' D3T sing 94 n n O4' C1' D3T sing 95 n n C1' N1 D3T sing 96 n n C1' C2' D3T sing 97 n n C1' H1' D3T sing 98 n n N1 C6 D3T sing 99 n n N1 C2 D3T sing 100 n n C6 C5 D3T doub 101 n n C6 H6 D3T sing 102 n n C2 O2 D3T doub 103 n n C2 N3 D3T sing 104 n n N3 C4 D3T sing 105 n n N3 HN3 D3T sing 106 n n C4 O4 D3T doub 107 n n C4 C5 D3T sing 108 n n C5 C5M D3T sing 109 n n C5M H5M1 D3T sing 110 n n C5M H5M2 D3T sing 111 n n C5M H5M3 D3T sing 112 n n C2' C3' D3T sing 113 n n C2' "H2'1" D3T sing 114 n n C2' "H2'2" D3T sing 115 n n C3' "H3'1" D3T sing 116 n n C3' "H3'2" D3T sing 117 n n O3A PB D3T sing 118 n n PB O1B D3T doub 119 n n PB O2B D3T sing 120 n n PB O3B D3T sing 121 n n O2B HOB2 D3T sing 122 n n O3B PG D3T sing 123 n n PG O1G D3T doub 124 n n PG O2G D3T sing 125 n n PG O3G D3T sing 126 n n O3G HOG3 D3T sing 127 n n HO1 O2G D3T sing 128 n n # _atom_sites.entry_id 3UXP _atom_sites.fract_transf_matrix[1][1] 0.009968 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002126 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017666 _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] 0.010978 _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 G 4 D3T A 1 336 1 D3T D3T . H 5 NA A 1 337 1 NA NA . I 5 NA A 1 338 2 NA NA . J 5 NA A 1 339 3 NA NA . K 5 NA A 1 340 6 NA NA . L 4 D3T B 1 336 1 D3T D3T . M 5 NA B 1 337 4 NA NA . N 5 NA B 1 338 5 NA NA . O 5 NA B 1 339 7 NA NA . P 6 HOH A 1 341 2 HOH HOH . P 6 HOH A 2 342 7 HOH HOH . P 6 HOH A 3 343 10 HOH HOH . P 6 HOH A 4 344 20 HOH HOH . P 6 HOH A 5 345 21 HOH HOH . P 6 HOH A 6 346 23 HOH HOH . P 6 HOH A 7 347 24 HOH HOH . P 6 HOH A 8 348 28 HOH HOH . P 6 HOH A 9 349 29 HOH HOH . P 6 HOH A 10 350 37 HOH HOH . P 6 HOH A 11 351 39 HOH HOH . P 6 HOH A 12 352 43 HOH HOH . P 6 HOH A 13 353 44 HOH HOH . Q 6 HOH B 1 340 1 HOH HOH . Q 6 HOH B 2 341 5 HOH HOH . Q 6 HOH B 3 342 6 HOH HOH . Q 6 HOH B 4 343 9 HOH HOH . Q 6 HOH B 5 344 11 HOH HOH . Q 6 HOH B 6 345 15 HOH HOH . Q 6 HOH B 7 346 22 HOH HOH . Q 6 HOH B 8 347 25 HOH HOH . Q 6 HOH B 9 348 26 HOH HOH . Q 6 HOH B 10 349 30 HOH HOH . Q 6 HOH B 11 350 31 HOH HOH . Q 6 HOH B 12 351 33 HOH HOH . Q 6 HOH B 13 352 35 HOH HOH . Q 6 HOH B 14 353 40 HOH HOH . Q 6 HOH B 15 354 41 HOH HOH . Q 6 HOH B 16 355 45 HOH HOH . Q 6 HOH B 17 356 47 HOH HOH . R 6 HOH P 1 14 14 HOH HOH . R 6 HOH P 2 34 34 HOH HOH . S 6 HOH T 1 12 12 HOH HOH . S 6 HOH T 2 18 18 HOH HOH . S 6 HOH T 3 36 36 HOH HOH . S 6 HOH T 4 46 46 HOH HOH . T 6 HOH D 1 19 19 HOH HOH . U 6 HOH E 1 12 3 HOH HOH . U 6 HOH E 2 13 4 HOH HOH . U 6 HOH E 3 17 17 HOH HOH . U 6 HOH E 4 38 38 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 D3T . . . L 4 41.484 9.494 -29.499 1 61.98 ? PA D3T 336 B 1 HETATM 2 O O1A D3T . . . L 4 40.472 10.372 -28.791 1 76.67 ? O1A D3T 336 B 1 HETATM 3 O O2A D3T . . . L 4 42.879 9.839 -29.073 1 51.89 ? O2A D3T 336 B 1 HETATM 4 O O5' D3T . . . L 4 41.315 9.534 -31.085 1 57.14 ? O5' D3T 336 B 1 HETATM 5 C C5' D3T . . . L 4 40.106 10.137 -31.539 1 62.66 ? C5' D3T 336 B 1 HETATM 6 C C4' D3T . . . L 4 39.589 9.358 -32.726 1 59.61 ? C4' D3T 336 B 1 HETATM 7 O O4' D3T . . . L 4 40.427 9.599 -33.862 1 60.68 ? O4' D3T 336 B 1 HETATM 8 C C1' D3T . . . L 4 40.663 8.378 -34.547 1 56.72 ? C1' D3T 336 B 1 HETATM 9 N N1 D3T . . . L 4 42.085 8.083 -34.657 1 56.22 ? N1 D3T 336 B 1 HETATM 10 C C6 D3T . . . L 4 42.935 8.293 -33.635 1 57.03 ? C6 D3T 336 B 1 HETATM 11 C C2 D3T . . . L 4 42.529 7.517 -35.865 1 74.23 ? C2 D3T 336 B 1 HETATM 12 O O2 D3T . . . L 4 41.689 7.332 -36.77 1 81.38 ? O2 D3T 336 B 1 HETATM 13 N N3 D3T . . . L 4 43.82 7.188 -36.061 1 76.24 ? N3 D3T 336 B 1 HETATM 14 C C4 D3T . . . L 4 44.725 7.379 -35.092 1 71.5 ? C4 D3T 336 B 1 HETATM 15 O O4 D3T . . . L 4 45.924 7.075 -35.271 1 66 ? O4 D3T 336 B 1 HETATM 16 C C5 D3T . . . L 4 44.286 7.966 -33.796 1 65.36 ? C5 D3T 336 B 1 HETATM 17 C C5M D3T . . . L 4 45.309 8.19 -32.704 1 49.42 ? C5M D3T 336 B 1 HETATM 18 C C2' D3T . . . L 4 40.058 7.255 -33.707 1 50.38 ? C2' D3T 336 B 1 HETATM 19 C C3' D3T . . . L 4 39.645 7.878 -32.395 1 47.01 ? C3' D3T 336 B 1 HETATM 20 O O3A D3T . . . L 4 41.132 7.967 -29.203 1 80.91 ? O3A D3T 336 B 1 HETATM 21 P PB D3T . . . L 4 40.065 7.692 -28.05 1 77.35 ? PB D3T 336 B 1 HETATM 22 O O1B D3T . . . L 4 38.774 8.313 -28.5 1 82.42 ? O1B D3T 336 B 1 HETATM 23 O O2B D3T . . . L 4 39.937 6.207 -27.843 1 85.99 ? O2B D3T 336 B 1 HETATM 24 O O3B D3T . . . L 4 40.664 8.476 -26.775 1 71.35 ? O3B D3T 336 B 1 HETATM 25 P PG D3T . . . L 4 40.717 7.931 -25.256 1 77.4 ? PG D3T 336 B 1 HETATM 26 O O1G D3T . . . L 4 40.55 6.429 -25.147 1 65.23 ? O1G D3T 336 B 1 HETATM 27 O O2G D3T . . . L 4 42.093 8.284 -24.731 1 74.39 ? O2G D3T 336 B 1 HETATM 28 O O3G D3T . . . L 4 39.699 8.604 -24.367 1 60.94 ? O3G D3T 336 B 1 # _model_server_stats.io_time_ms 25 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #