data_5F9K # _model_server_result.job_id 7SYj218KtLnzN_FeAYDbdw _model_server_result.datetime_utc '2024-10-19 16:22:58' _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 5f9k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":201}' # _entry.id 5F9K # _exptl.entry_id 5F9K _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 467.157 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 3 _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 5F9K _cell.length_a 71.633 _cell.length_b 72.458 _cell.length_c 75.158 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5F9K _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_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 _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 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 D N N ? 2 E N N ? 2 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 B O ILE 61 B ILE 61 1_555 H MG MG . B MG 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.921 ? metalc ? metalc2 B OD2 ASP 81 B ASP 81 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.712 ? metalc ? metalc3 E O2B DUP . B DUP 201 1_555 G MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc4 H MG MG . B MG 204 1_555 N O HOH . B HOH 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.979 ? metalc ? metalc5 H MG MG . B MG 204 1_555 N O HOH . B HOH 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? metalc ? metalc6 I MG MG . B MG 205 1_555 N O HOH . B HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc7 N O HOH . B HOH 315 1_555 J MG MG . C MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.809 ? metalc ? metalc8 J MG MG . C MG 201 1_555 O O HOH . C HOH 337 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.708 ? # _chem_comp.formula 'C9 H16 N3 O13 P3' _chem_comp.formula_weight 467.157 _chem_comp.id DUP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-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 O4 C4 DUP doub 83 n n C4 C5 DUP sing 84 n y C4 N3 DUP sing 85 n y C5 C6 DUP doub 86 n y C5 H5 DUP sing 87 n n C6 N1 DUP sing 88 n y C6 H6 DUP sing 89 n n N3 C2 DUP sing 90 n y N3 HN3 DUP sing 91 n n C2 O2 DUP doub 92 n n C2 N1 DUP sing 93 n y N1 C1' DUP sing 94 n n C1' C2' DUP sing 95 n n C1' O4' DUP sing 96 n n C1' H1' DUP sing 97 n n C2' C3' DUP sing 98 n n C2' "H2'1" DUP sing 99 n n C2' "H2'2" DUP sing 100 n n C3' O3' DUP sing 101 n n C3' C4' DUP sing 102 n n C3' H1 DUP sing 103 n n O3' H3' DUP sing 104 n n O4' C4' DUP sing 105 n n C4' C5' DUP sing 106 n n C4' H4' DUP sing 107 n n C5' O5' DUP sing 108 n n C5' "H5'1" DUP sing 109 n n C5' "H5'2" DUP sing 110 n n O5' PA DUP sing 111 n n PA O1A DUP doub 112 n n PA O2A DUP sing 113 n n PA N3A DUP sing 114 n n O2A H2A DUP sing 115 n n N3A PB DUP sing 116 n n N3A H3A DUP sing 117 n n PB O1B DUP doub 118 n n PB O2B DUP sing 119 n n PB O3B DUP sing 120 n n O2B H2B DUP sing 121 n n O3B PG DUP sing 122 n n PG O2G DUP doub 123 n n PG O1G DUP sing 124 n n PG O3G DUP sing 125 n n O1G H1G DUP sing 126 n n O3G H3G DUP sing 127 n n # _atom_sites.entry_id 5F9K _atom_sites.fract_transf_matrix[1][1] 0.01396 _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] 0.013801 _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] 0.013305 _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 D 2 DUP A 1 201 1 DUP DUP . E 2 DUP B 1 201 1 DUP DUP . F 3 MG B 1 202 4 MG MG . G 3 MG B 1 203 7 MG MG . H 3 MG B 1 204 9 MG MG . I 3 MG B 1 205 10 MG MG . J 3 MG C 1 201 8 MG MG . K 4 SO4 C 1 202 1 SO4 SO4 . L 2 DUP C 1 203 1 DUP DUP . M 5 HOH A 1 301 134 HOH HOH . M 5 HOH A 2 302 89 HOH HOH . M 5 HOH A 3 303 133 HOH HOH . M 5 HOH A 4 304 75 HOH HOH . M 5 HOH A 5 305 130 HOH HOH . M 5 HOH A 6 306 136 HOH HOH . M 5 HOH A 7 307 100 HOH HOH . M 5 HOH A 8 308 48 HOH HOH . M 5 HOH A 9 309 4 HOH HOH . M 5 HOH A 10 310 44 HOH HOH . M 5 HOH A 11 311 137 HOH HOH . M 5 HOH A 12 312 80 HOH HOH . M 5 HOH A 13 313 86 HOH HOH . M 5 HOH A 14 314 51 HOH HOH . M 5 HOH A 15 315 102 HOH HOH . M 5 HOH A 16 316 5 HOH HOH . M 5 HOH A 17 317 25 HOH HOH . M 5 HOH A 18 318 47 HOH HOH . M 5 HOH A 19 319 119 HOH HOH . M 5 HOH A 20 320 67 HOH HOH . M 5 HOH A 21 321 20 HOH HOH . M 5 HOH A 22 322 97 HOH HOH . M 5 HOH A 23 323 63 HOH HOH . M 5 HOH A 24 324 18 HOH HOH . M 5 HOH A 25 325 1 HOH HOH . M 5 HOH A 26 326 34 HOH HOH . M 5 HOH A 27 327 99 HOH HOH . M 5 HOH A 28 328 72 HOH HOH . M 5 HOH A 29 329 83 HOH HOH . M 5 HOH A 30 330 147 HOH HOH . M 5 HOH A 31 331 143 HOH HOH . M 5 HOH A 32 332 7 HOH HOH . M 5 HOH A 33 333 103 HOH HOH . M 5 HOH A 34 334 110 HOH HOH . M 5 HOH A 35 335 50 HOH HOH . M 5 HOH A 36 336 152 HOH HOH . M 5 HOH A 37 337 93 HOH HOH . M 5 HOH A 38 338 95 HOH HOH . M 5 HOH A 39 339 87 HOH HOH . M 5 HOH A 40 340 132 HOH HOH . M 5 HOH A 41 341 164 HOH HOH . M 5 HOH A 42 342 40 HOH HOH . M 5 HOH A 43 343 62 HOH HOH . M 5 HOH A 44 344 19 HOH HOH . M 5 HOH A 45 345 69 HOH HOH . M 5 HOH A 46 346 88 HOH HOH . M 5 HOH A 47 347 71 HOH HOH . M 5 HOH A 48 348 77 HOH HOH . M 5 HOH A 49 349 157 HOH HOH . M 5 HOH A 50 350 112 HOH HOH . M 5 HOH A 51 351 129 HOH HOH . M 5 HOH A 52 352 120 HOH HOH . M 5 HOH A 53 353 158 HOH HOH . M 5 HOH A 54 354 117 HOH HOH . M 5 HOH A 55 355 101 HOH HOH . M 5 HOH A 56 356 107 HOH HOH . M 5 HOH A 57 357 156 HOH HOH . M 5 HOH A 58 358 114 HOH HOH . M 5 HOH A 59 359 153 HOH HOH . N 5 HOH B 1 301 128 HOH HOH . N 5 HOH B 2 302 60 HOH HOH . N 5 HOH B 3 303 31 HOH HOH . N 5 HOH B 4 304 74 HOH HOH . N 5 HOH B 5 305 42 HOH HOH . N 5 HOH B 6 306 54 HOH HOH . N 5 HOH B 7 307 125 HOH HOH . N 5 HOH B 8 308 29 HOH HOH . N 5 HOH B 9 309 92 HOH HOH . N 5 HOH B 10 310 66 HOH HOH . N 5 HOH B 11 311 53 HOH HOH . N 5 HOH B 12 312 33 HOH HOH . N 5 HOH B 13 313 30 HOH HOH . N 5 HOH B 14 314 21 HOH HOH . N 5 HOH B 15 315 32 HOH HOH . N 5 HOH B 16 316 70 HOH HOH . N 5 HOH B 17 317 38 HOH HOH . N 5 HOH B 18 318 154 HOH HOH . N 5 HOH B 19 319 14 HOH HOH . N 5 HOH B 20 320 8 HOH HOH . N 5 HOH B 21 321 37 HOH HOH . N 5 HOH B 22 322 15 HOH HOH . N 5 HOH B 23 323 23 HOH HOH . N 5 HOH B 24 324 106 HOH HOH . N 5 HOH B 25 325 65 HOH HOH . N 5 HOH B 26 326 56 HOH HOH . N 5 HOH B 27 327 10 HOH HOH . N 5 HOH B 28 328 13 HOH HOH . N 5 HOH B 29 329 22 HOH HOH . N 5 HOH B 30 330 81 HOH HOH . N 5 HOH B 31 331 6 HOH HOH . N 5 HOH B 32 332 155 HOH HOH . N 5 HOH B 33 333 141 HOH HOH . N 5 HOH B 34 334 104 HOH HOH . N 5 HOH B 35 335 166 HOH HOH . N 5 HOH B 36 336 55 HOH HOH . N 5 HOH B 37 337 127 HOH HOH . N 5 HOH B 38 338 46 HOH HOH . N 5 HOH B 39 339 35 HOH HOH . N 5 HOH B 40 340 122 HOH HOH . N 5 HOH B 41 341 161 HOH HOH . N 5 HOH B 42 342 126 HOH HOH . N 5 HOH B 43 343 111 HOH HOH . N 5 HOH B 44 344 108 HOH HOH . N 5 HOH B 45 345 140 HOH HOH . N 5 HOH B 46 346 139 HOH HOH . N 5 HOH B 47 347 163 HOH HOH . N 5 HOH B 48 348 76 HOH HOH . O 5 HOH C 1 301 144 HOH HOH . O 5 HOH C 2 302 131 HOH HOH . O 5 HOH C 3 303 59 HOH HOH . O 5 HOH C 4 304 64 HOH HOH . O 5 HOH C 5 305 146 HOH HOH . O 5 HOH C 6 306 12 HOH HOH . O 5 HOH C 7 307 148 HOH HOH . O 5 HOH C 8 308 26 HOH HOH . O 5 HOH C 9 309 9 HOH HOH . O 5 HOH C 10 310 94 HOH HOH . O 5 HOH C 11 311 160 HOH HOH . O 5 HOH C 12 312 167 HOH HOH . O 5 HOH C 13 313 142 HOH HOH . O 5 HOH C 14 314 57 HOH HOH . O 5 HOH C 15 315 90 HOH HOH . O 5 HOH C 16 316 145 HOH HOH . O 5 HOH C 17 317 45 HOH HOH . O 5 HOH C 18 318 2 HOH HOH . O 5 HOH C 19 319 41 HOH HOH . O 5 HOH C 20 320 16 HOH HOH . O 5 HOH C 21 321 79 HOH HOH . O 5 HOH C 22 322 78 HOH HOH . O 5 HOH C 23 323 24 HOH HOH . O 5 HOH C 24 324 39 HOH HOH . O 5 HOH C 25 325 96 HOH HOH . O 5 HOH C 26 326 58 HOH HOH . O 5 HOH C 27 327 82 HOH HOH . O 5 HOH C 28 328 151 HOH HOH . O 5 HOH C 29 329 85 HOH HOH . O 5 HOH C 30 330 135 HOH HOH . O 5 HOH C 31 331 17 HOH HOH . O 5 HOH C 32 332 36 HOH HOH . O 5 HOH C 33 333 68 HOH HOH . O 5 HOH C 34 334 43 HOH HOH . O 5 HOH C 35 335 11 HOH HOH . O 5 HOH C 36 336 3 HOH HOH . O 5 HOH C 37 337 61 HOH HOH . O 5 HOH C 38 338 113 HOH HOH . O 5 HOH C 39 339 28 HOH HOH . O 5 HOH C 40 340 109 HOH HOH . O 5 HOH C 41 341 27 HOH HOH . O 5 HOH C 42 342 49 HOH HOH . O 5 HOH C 43 343 162 HOH HOH . O 5 HOH C 44 344 91 HOH HOH . O 5 HOH C 45 345 52 HOH HOH . O 5 HOH C 46 346 138 HOH HOH . O 5 HOH C 47 347 98 HOH HOH . O 5 HOH C 48 348 105 HOH HOH . O 5 HOH C 49 349 165 HOH HOH . O 5 HOH C 50 350 149 HOH HOH . O 5 HOH C 51 351 116 HOH HOH . O 5 HOH C 52 352 118 HOH HOH . O 5 HOH C 53 353 73 HOH HOH . O 5 HOH C 54 354 159 HOH HOH . O 5 HOH C 55 355 150 HOH HOH . O 5 HOH C 56 356 124 HOH HOH . O 5 HOH C 57 357 84 HOH HOH . O 5 HOH C 58 358 115 HOH HOH . O 5 HOH C 59 359 121 HOH HOH . O 5 HOH C 60 360 123 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 O O4 DUP . . . E 2 40.121 -9.716 -10.591 1 73.35 ? O4 DUP 201 B 1 HETATM 2 C C4 DUP . . . E 2 40.354 -10.105 -11.759 1 73.01 ? C4 DUP 201 B 1 HETATM 3 C C5 DUP . . . E 2 39.992 -9.332 -12.802 1 72.42 ? C5 DUP 201 B 1 HETATM 4 C C6 DUP . . . E 2 40.256 -9.755 -14.07 1 78.79 ? C6 DUP 201 B 1 HETATM 5 N N3 DUP . . . E 2 40.955 -11.265 -11.987 1 71.12 ? N3 DUP 201 B 1 HETATM 6 C C2 DUP . . . E 2 41.213 -11.689 -13.249 1 76.08 ? C2 DUP 201 B 1 HETATM 7 O O2 DUP . . . E 2 41.765 -12.749 -13.351 1 74.48 ? O2 DUP 201 B 1 HETATM 8 N N1 DUP . . . E 2 40.849 -10.916 -14.319 1 80.56 ? N1 DUP 201 B 1 HETATM 9 C C1' DUP . . . E 2 41.023 -11.218 -15.568 1 82.99 ? C1' DUP 201 B 1 HETATM 10 C C2' DUP . . . E 2 40.578 -12.631 -15.967 1 87.48 ? C2' DUP 201 B 1 HETATM 11 C C3' DUP . . . E 2 39.28 -12.563 -16.167 1 87.95 ? C3' DUP 201 B 1 HETATM 12 O O3' DUP . . . E 2 38.887 -13.578 -17.13 1 90.71 ? O3' DUP 201 B 1 HETATM 13 O O4' DUP . . . E 2 40.037 -10.34 -16.436 1 86.55 ? O4' DUP 201 B 1 HETATM 14 C C4' DUP . . . E 2 38.983 -11.049 -16.722 1 89.5 ? C4' DUP 201 B 1 HETATM 15 C C5' DUP . . . E 2 37.725 -10.445 -16.121 1 86.09 ? C5' DUP 201 B 1 HETATM 16 O O5' DUP . . . E 2 36.512 -11.089 -16.58 1 92.65 ? O5' DUP 201 B 1 HETATM 17 P PA DUP . . . E 2 35.084 -10.844 -15.872 1 102.93 ? PA DUP 201 B 1 HETATM 18 O O1A DUP . . . E 2 34.205 -12.077 -16.094 1 102.55 ? O1A DUP 201 B 1 HETATM 19 O O2A DUP . . . E 2 35.216 -10.643 -14.334 1 89.23 ? O2A DUP 201 B 1 HETATM 20 N N3A DUP . . . E 2 34.334 -9.494 -16.602 1 92.32 ? N3A DUP 201 B 1 HETATM 21 P PB DUP . . . E 2 33.377 -8.367 -15.791 1 92.12 ? PB DUP 201 B 1 HETATM 22 O O1B DUP . . . E 2 34.15 -7.057 -15.67 1 74.45 ? O1B DUP 201 B 1 HETATM 23 O O2B DUP . . . E 2 32.935 -8.9 -14.382 1 83.22 ? O2B DUP 201 B 1 HETATM 24 O O3B DUP . . . E 2 32.051 -8.051 -16.692 1 95.08 ? O3B DUP 201 B 1 HETATM 25 P PG DUP . . . E 2 30.924 -9.017 -17.009 1 110.61 ? PG DUP 201 B 1 HETATM 26 O O2G DUP . . . E 2 31.142 -9.62 -18.378 1 98.85 ? O2G DUP 201 B 1 HETATM 27 O O1G DUP . . . E 2 30.86 -10.096 -15.97 1 99.88 -1 O1G DUP 201 B 1 HETATM 28 O O3G DUP . . . E 2 29.654 -8.264 -17.017 1 90.46 ? O3G DUP 201 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 220 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #