data_1LWX # _model_server_result.job_id bdwMx_OnuypUAuCavp-eVw _model_server_result.datetime_utc '2024-10-19 00:55:45' _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 1lwx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":156}' # _entry.id 1LWX # _exptl.entry_id 1LWX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "3'-AZIDO-3'-DEOXYTHYMIDINE-5'-DIPHOSPHATE" _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 120 _cell.entry_id 1LWX _cell.length_a 71.59 _cell.length_b 71.59 _cell.length_c 152.7 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1LWX _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31 2 1' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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' 6_765 -x+2,-x+y+1,-z+1/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 107.385 61.998759 50.9 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 F N N ? 3 H 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 E O1B AZD . A AZD 156 1_555 D MG MG . A MG 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.523 ? metalc ? metalc2 E O1A AZD . A AZD 156 1_555 D MG MG . A MG 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc3 D MG MG . A MG 157 1_555 I O HOH . A HOH 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc4 D MG MG . A MG 157 1_555 I O HOH . A HOH 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? metalc ? metalc5 H O1B AZD . C AZD 156 1_555 G MG MG . C MG 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.62 ? metalc ? metalc6 H O1A AZD . C AZD 156 1_555 G MG MG . C MG 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.784 ? metalc ? metalc7 G MG MG . C MG 157 1_555 K O HOH . C HOH 231 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc8 G MG MG . C MG 157 1_555 K O HOH . C HOH 281 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id AZD _chem_comp.mon_nstd_flag . _chem_comp.name "3'-AZIDO-3'-DEOXYTHYMIDINE-5'-DIPHOSPHATE" _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 AZD doub 70 n n PA O2A AZD sing 71 n n PA O3A AZD sing 72 n n PA O5' AZD sing 73 n n O2A HOA2 AZD sing 74 n n O3A PB AZD sing 75 n n PB O1B AZD doub 76 n n PB O2B AZD sing 77 n n PB O3B AZD sing 78 n n O2B HOB2 AZD sing 79 n n O3B HOB3 AZD sing 80 n n O5' C5' AZD sing 81 n n C5' C4' AZD sing 82 n n C5' "H5'1" AZD sing 83 n n C5' "H5'2" AZD sing 84 n n C4' O4' AZD sing 85 n n C4' C3' AZD sing 86 n n C4' H4' AZD sing 87 n n O4' C1' AZD sing 88 n n C3' N3' AZD sing 89 n n C3' C2' AZD sing 90 n n C3' H3' AZD sing 91 n n N3' N4' AZD doub 92 n n N4' N5' AZD doub 93 n n C2' C1' AZD sing 94 n n C2' "H2'1" AZD sing 95 n n C2' "H2'2" AZD sing 96 n n C1' N1 AZD sing 97 n n C1' H1' AZD sing 98 n n N1 C2 AZD sing 99 n n N1 C6 AZD sing 100 n n C2 O2 AZD doub 101 n n C2 N3 AZD sing 102 n n N3 C4 AZD sing 103 n n N3 HN3 AZD sing 104 n n C4 O4 AZD doub 105 n n C4 C5 AZD sing 106 n n C5 C5A AZD sing 107 n n C5 C6 AZD doub 108 n n C5A H51 AZD sing 109 n n C5A H52 AZD sing 110 n n C5A H53 AZD sing 111 n n C6 H6 AZD sing 112 n n # _atom_sites.entry_id 1LWX _atom_sites.fract_transf_matrix[1][1] 0.013968 _atom_sites.fract_transf_matrix[1][2] 0.008065 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016129 _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] 0.006549 _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 MG A 1 157 157 MG MG . E 3 AZD A 1 156 156 AZD AZD . F 3 AZD B 1 156 156 AZD AZD . G 2 MG C 1 157 157 MG MG . H 3 AZD C 1 156 156 AZD AZD . I 4 HOH A 1 210 210 HOH HOH . I 4 HOH A 2 217 217 HOH HOH . I 4 HOH A 3 220 220 HOH HOH . I 4 HOH A 4 224 224 HOH HOH . I 4 HOH A 5 230 230 HOH HOH . I 4 HOH A 6 233 233 HOH HOH . I 4 HOH A 7 234 234 HOH HOH . I 4 HOH A 8 239 239 HOH HOH . I 4 HOH A 9 241 241 HOH HOH . I 4 HOH A 10 245 245 HOH HOH . I 4 HOH A 11 246 246 HOH HOH . I 4 HOH A 12 249 249 HOH HOH . I 4 HOH A 13 250 250 HOH HOH . I 4 HOH A 14 252 252 HOH HOH . I 4 HOH A 15 253 253 HOH HOH . I 4 HOH A 16 260 260 HOH HOH . I 4 HOH A 17 269 269 HOH HOH . I 4 HOH A 18 274 274 HOH HOH . I 4 HOH A 19 275 275 HOH HOH . I 4 HOH A 20 276 276 HOH HOH . I 4 HOH A 21 278 278 HOH HOH . I 4 HOH A 22 279 279 HOH HOH . I 4 HOH A 23 280 280 HOH HOH . I 4 HOH A 24 282 282 HOH HOH . I 4 HOH A 25 283 283 HOH HOH . I 4 HOH A 26 285 285 HOH HOH . I 4 HOH A 27 288 288 HOH HOH . I 4 HOH A 28 294 294 HOH HOH . I 4 HOH A 29 301 301 HOH HOH . I 4 HOH A 30 302 302 HOH HOH . I 4 HOH A 31 303 303 HOH HOH . I 4 HOH A 32 306 306 HOH HOH . I 4 HOH A 33 307 307 HOH HOH . I 4 HOH A 34 309 309 HOH HOH . I 4 HOH A 35 310 310 HOH HOH . I 4 HOH A 36 311 311 HOH HOH . I 4 HOH A 37 312 312 HOH HOH . I 4 HOH A 38 322 322 HOH HOH . I 4 HOH A 39 325 325 HOH HOH . I 4 HOH A 40 326 326 HOH HOH . I 4 HOH A 41 331 331 HOH HOH . I 4 HOH A 42 335 335 HOH HOH . J 4 HOH B 1 202 202 HOH HOH . J 4 HOH B 2 205 205 HOH HOH . J 4 HOH B 3 206 206 HOH HOH . J 4 HOH B 4 209 209 HOH HOH . J 4 HOH B 5 211 211 HOH HOH . J 4 HOH B 6 212 212 HOH HOH . J 4 HOH B 7 213 213 HOH HOH . J 4 HOH B 8 215 215 HOH HOH . J 4 HOH B 9 216 216 HOH HOH . J 4 HOH B 10 218 218 HOH HOH . J 4 HOH B 11 222 222 HOH HOH . J 4 HOH B 12 225 225 HOH HOH . J 4 HOH B 13 226 226 HOH HOH . J 4 HOH B 14 227 227 HOH HOH . J 4 HOH B 15 228 228 HOH HOH . J 4 HOH B 16 229 229 HOH HOH . J 4 HOH B 17 232 232 HOH HOH . J 4 HOH B 18 235 235 HOH HOH . J 4 HOH B 19 240 240 HOH HOH . J 4 HOH B 20 242 242 HOH HOH . J 4 HOH B 21 243 243 HOH HOH . J 4 HOH B 22 251 251 HOH HOH . J 4 HOH B 23 254 254 HOH HOH . J 4 HOH B 24 255 255 HOH HOH . J 4 HOH B 25 259 259 HOH HOH . J 4 HOH B 26 261 261 HOH HOH . J 4 HOH B 27 263 263 HOH HOH . J 4 HOH B 28 271 271 HOH HOH . J 4 HOH B 29 284 284 HOH HOH . J 4 HOH B 30 286 286 HOH HOH . J 4 HOH B 31 290 290 HOH HOH . J 4 HOH B 32 291 291 HOH HOH . J 4 HOH B 33 293 293 HOH HOH . J 4 HOH B 34 296 296 HOH HOH . J 4 HOH B 35 297 297 HOH HOH . J 4 HOH B 36 299 299 HOH HOH . J 4 HOH B 37 300 300 HOH HOH . J 4 HOH B 38 304 304 HOH HOH . J 4 HOH B 39 308 308 HOH HOH . J 4 HOH B 40 316 316 HOH HOH . J 4 HOH B 41 317 317 HOH HOH . J 4 HOH B 42 319 319 HOH HOH . J 4 HOH B 43 320 320 HOH HOH . J 4 HOH B 44 321 321 HOH HOH . J 4 HOH B 45 323 323 HOH HOH . J 4 HOH B 46 327 327 HOH HOH . J 4 HOH B 47 329 329 HOH HOH . J 4 HOH B 48 330 330 HOH HOH . J 4 HOH B 49 332 332 HOH HOH . J 4 HOH B 50 333 333 HOH HOH . J 4 HOH B 51 337 337 HOH HOH . J 4 HOH B 52 338 338 HOH HOH . J 4 HOH B 53 339 339 HOH HOH . K 4 HOH C 1 200 200 HOH HOH . K 4 HOH C 2 201 201 HOH HOH . K 4 HOH C 3 203 203 HOH HOH . K 4 HOH C 4 204 204 HOH HOH . K 4 HOH C 5 207 207 HOH HOH . K 4 HOH C 6 208 208 HOH HOH . K 4 HOH C 7 214 214 HOH HOH . K 4 HOH C 8 219 219 HOH HOH . K 4 HOH C 9 221 221 HOH HOH . K 4 HOH C 10 223 223 HOH HOH . K 4 HOH C 11 231 231 HOH HOH . K 4 HOH C 12 236 236 HOH HOH . K 4 HOH C 13 237 237 HOH HOH . K 4 HOH C 14 238 238 HOH HOH . K 4 HOH C 15 244 244 HOH HOH . K 4 HOH C 16 247 247 HOH HOH . K 4 HOH C 17 248 248 HOH HOH . K 4 HOH C 18 256 256 HOH HOH . K 4 HOH C 19 257 257 HOH HOH . K 4 HOH C 20 258 258 HOH HOH . K 4 HOH C 21 262 262 HOH HOH . K 4 HOH C 22 264 264 HOH HOH . K 4 HOH C 23 265 265 HOH HOH . K 4 HOH C 24 266 266 HOH HOH . K 4 HOH C 25 267 267 HOH HOH . K 4 HOH C 26 268 268 HOH HOH . K 4 HOH C 27 270 270 HOH HOH . K 4 HOH C 28 272 272 HOH HOH . K 4 HOH C 29 273 273 HOH HOH . K 4 HOH C 30 277 277 HOH HOH . K 4 HOH C 31 281 281 HOH HOH . K 4 HOH C 32 287 287 HOH HOH . K 4 HOH C 33 289 289 HOH HOH . K 4 HOH C 34 292 292 HOH HOH . K 4 HOH C 35 295 295 HOH HOH . K 4 HOH C 36 298 298 HOH HOH . K 4 HOH C 37 305 305 HOH HOH . K 4 HOH C 38 313 313 HOH HOH . K 4 HOH C 39 314 314 HOH HOH . K 4 HOH C 40 315 315 HOH HOH . K 4 HOH C 41 318 318 HOH HOH . K 4 HOH C 42 324 324 HOH HOH . K 4 HOH C 43 328 328 HOH HOH . K 4 HOH C 44 334 334 HOH HOH . K 4 HOH C 45 336 336 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 AZD . . . H 3 49.464 2.366 9.093 1 25.12 ? PA AZD 156 C 1 HETATM 2 O O1A AZD . . . H 3 48.175 1.901 9.636 1 28.54 ? O1A AZD 156 C 1 HETATM 3 O O2A AZD . . . H 3 49.695 2.417 7.638 1 23.72 ? O2A AZD 156 C 1 HETATM 4 O O3A AZD . . . H 3 49.826 3.852 9.689 1 24.85 ? O3A AZD 156 C 1 HETATM 5 P PB AZD . . . H 3 49.011 5.02 10.486 1 21.49 ? PB AZD 156 C 1 HETATM 6 O O1B AZD . . . H 3 47.58 4.771 10.331 1 24.86 ? O1B AZD 156 C 1 HETATM 7 O O2B AZD . . . H 3 49.31 6.278 9.77 1 19.49 ? O2B AZD 156 C 1 HETATM 8 O O3B AZD . . . H 3 49.347 4.858 11.936 1 23.64 ? O3B AZD 156 C 1 HETATM 9 O O5' AZD . . . H 3 50.55 1.426 9.8 1 28.77 ? O5' AZD 156 C 1 HETATM 10 C C5' AZD . . . H 3 50.239 1.142 11.225 1 30.49 ? C5' AZD 156 C 1 HETATM 11 C C4' AZD . . . H 3 51.437 1.182 12.176 1 30.93 ? C4' AZD 156 C 1 HETATM 12 O O4' AZD . . . H 3 52.265 0.465 11.266 1 27.85 ? O4' AZD 156 C 1 HETATM 13 C C3' AZD . . . H 3 52.134 2.532 12.433 1 30.61 ? C3' AZD 156 C 1 HETATM 14 N N3' AZD . . . H 3 52.484 2.804 13.889 1 33.35 ? N3' AZD 156 C 1 HETATM 15 N N4' AZD . . . H 3 51.749 3.648 14.396 1 27.38 ? N4' AZD 156 C 1 HETATM 16 N N5' AZD . . . H 3 50.937 4.304 14.766 1 23.89 ? N5' AZD 156 C 1 HETATM 17 C C2' AZD . . . H 3 53.295 2.578 11.466 1 32.28 ? C2' AZD 156 C 1 HETATM 18 C C1' AZD . . . H 3 53.526 1.1 11.053 1 34.77 ? C1' AZD 156 C 1 HETATM 19 N N1 AZD . . . H 3 54.005 0.716 9.642 1 36.66 ? N1 AZD 156 C 1 HETATM 20 C C2 AZD . . . H 3 55.371 0.391 9.448 1 39.89 ? C2 AZD 156 C 1 HETATM 21 O O2 AZD . . . H 3 56.167 0.131 10.347 1 41.39 ? O2 AZD 156 C 1 HETATM 22 N N3 AZD . . . H 3 55.836 0.396 8.149 1 37.32 ? N3 AZD 156 C 1 HETATM 23 C C4 AZD . . . H 3 55.08 0.68 7.065 1 35.45 ? C4 AZD 156 C 1 HETATM 24 O O4 AZD . . . H 3 55.615 0.702 5.992 1 39.01 ? O4 AZD 156 C 1 HETATM 25 C C5 AZD . . . H 3 53.722 0.964 7.297 1 33.15 ? C5 AZD 156 C 1 HETATM 26 C C5A AZD . . . H 3 52.785 1.108 6.112 1 37.9 ? C5A AZD 156 C 1 HETATM 27 C C6 AZD . . . H 3 53.237 0.985 8.542 1 37.6 ? C6 AZD 156 C 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 358 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #