data_2Z6Q # _model_server_result.job_id 8-f8WdOtUBeUJ1DM_r7NHg _model_server_result.datetime_utc '2024-10-19 11:25:05' _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 2z6q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":427}' # _entry.id 2Z6Q # _exptl.entry_id 2Z6Q _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 227.217 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYCYTIDINE" _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 120 _cell.entry_id 2Z6Q _cell.length_a 92.924 _cell.length_b 92.924 _cell.length_c 315.781 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2Z6Q _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I _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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _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 covale ? covale1 B O3' DG 6 D DG 426 1_555 E O5' DCZ . A DCZ 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? hydrog WATSON-CRICK hydrog1 A N1 DG 1 C DG 402 1_555 C N3 DC 6 E DC 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N2 DG 1 C DG 402 1_555 C O2 DC 6 E DC 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O6 DG 1 C DG 402 1_555 C N4 DC 6 E DC 433 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 DA 2 C DA 403 1_555 C N3 DT 5 E DT 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N6 DA 2 C DA 403 1_555 C O4 DT 5 E DT 432 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A N3 DT 3 C DT 404 1_555 C N1 DA 4 E DA 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A O4 DT 3 C DT 404 1_555 C N6 DA 4 E DA 431 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N1 DA 4 C DA 405 1_555 C N3 DT 3 E DT 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A N6 DA 4 C DA 405 1_555 C O4 DT 3 E DT 430 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N1 DG 5 C DG 406 1_555 C N3 DC 2 E DC 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N2 DG 5 C DG 406 1_555 C O2 DC 2 E DC 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O6 DG 5 C DG 406 1_555 C N4 DC 2 E DC 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N3 DC 6 C DC 407 1_555 C N1 DG 1 E DG 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N4 DC 6 C DC 407 1_555 C O6 DG 1 E DG 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A O2 DC 6 C DC 407 1_555 C N2 DG 1 E DG 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N3 DC 8 C DC 409 1_555 B N1 DG 6 D DG 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N4 DC 8 C DC 409 1_555 B O6 DG 6 D DG 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A O2 DC 8 C DC 409 1_555 B N2 DG 6 D DG 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 A N3 DT 9 C DT 410 1_555 B N1 DA 5 D DA 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 A O4 DT 9 C DT 410 1_555 B N6 DA 5 D DA 425 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 A N1 DA 10 C DA 411 1_555 B N3 DT 4 D DT 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 A N6 DA 10 C DA 411 1_555 B O4 DT 4 D DT 424 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 A N3 DT 11 C DT 412 1_555 B N1 DA 3 D DA 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 A O4 DT 11 C DT 412 1_555 B N6 DA 3 D DA 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 A N3 DC 12 C DC 413 1_555 B N1 DG 2 D DG 422 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 A N4 DC 12 C DC 413 1_555 B O6 DG 2 D DG 422 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 A O2 DC 12 C DC 413 1_555 B N2 DG 2 D DG 422 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C9 H13 N3 O4' _chem_comp.formula_weight 227.217 _chem_comp.id DCZ _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYCYTIDINE" _chem_comp.type 'dna oh 5 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 N1 C2 DCZ sing 156 n n N1 C6 DCZ sing 157 n n N1 C1' DCZ sing 158 n n C2 N3 DCZ sing 159 n n C2 O2 DCZ doub 160 n n N3 C4 DCZ doub 161 n n C4 C5 DCZ sing 162 n n C4 N4 DCZ sing 163 n n C5 C6 DCZ doub 164 n n C5 H5 DCZ sing 165 n n C6 H6 DCZ sing 166 n n N4 HN41 DCZ sing 167 n n N4 HN42 DCZ sing 168 n n C1' C2' DCZ sing 169 n n C1' O4' DCZ sing 170 n n C1' H1' DCZ sing 171 n n C2' C3' DCZ sing 172 n n C2' "H2'1" DCZ sing 173 n n C2' "H2'2" DCZ sing 174 n n C3' C4' DCZ sing 175 n n C3' O3' DCZ sing 176 n n C3' H3' DCZ sing 177 n n C4' O4' DCZ sing 178 n n C4' C5' DCZ sing 179 n n C4' H4' DCZ sing 180 n n O3' HO3' DCZ sing 181 n n C5' O5' DCZ sing 182 n n C5' "H5'1" DCZ sing 183 n n C5' "H5'2" DCZ sing 184 n n O5' HO51 DCZ sing 185 n n # _atom_sites.entry_id 2Z6Q _atom_sites.fract_transf_matrix[1][1] 0.010761 _atom_sites.fract_transf_matrix[1][2] 0.006213 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012426 _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] 0.003167 _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 E 5 DCZ A 1 427 427 DCZ CYT . F 6 SAH A 1 328 328 SAH SAH . G 7 HOH C 1 335 335 HOH HOH . G 7 HOH C 2 359 359 HOH HOH . G 7 HOH C 3 368 368 HOH HOH . G 7 HOH C 4 389 389 HOH HOH . G 7 HOH C 5 395 395 HOH HOH . H 7 HOH E 1 334 334 HOH HOH . H 7 HOH E 2 347 347 HOH HOH . H 7 HOH E 3 399 399 HOH HOH . I 7 HOH A 1 329 329 HOH HOH . I 7 HOH A 2 330 330 HOH HOH . I 7 HOH A 3 331 331 HOH HOH . I 7 HOH A 4 332 332 HOH HOH . I 7 HOH A 5 333 333 HOH HOH . I 7 HOH A 6 336 336 HOH HOH . I 7 HOH A 7 337 337 HOH HOH . I 7 HOH A 8 338 338 HOH HOH . I 7 HOH A 9 339 339 HOH HOH . I 7 HOH A 10 340 340 HOH HOH . I 7 HOH A 11 341 341 HOH HOH . I 7 HOH A 12 342 342 HOH HOH . I 7 HOH A 13 343 343 HOH HOH . I 7 HOH A 14 344 344 HOH HOH . I 7 HOH A 15 345 345 HOH HOH . I 7 HOH A 16 346 346 HOH HOH . I 7 HOH A 17 348 348 HOH HOH . I 7 HOH A 18 349 349 HOH HOH . I 7 HOH A 19 350 350 HOH HOH . I 7 HOH A 20 351 351 HOH HOH . I 7 HOH A 21 352 352 HOH HOH . I 7 HOH A 22 353 353 HOH HOH . I 7 HOH A 23 354 354 HOH HOH . I 7 HOH A 24 355 355 HOH HOH . I 7 HOH A 25 356 356 HOH HOH . I 7 HOH A 26 357 357 HOH HOH . I 7 HOH A 27 358 358 HOH HOH . I 7 HOH A 28 360 360 HOH HOH . I 7 HOH A 29 361 361 HOH HOH . I 7 HOH A 30 362 362 HOH HOH . I 7 HOH A 31 363 363 HOH HOH . I 7 HOH A 32 364 364 HOH HOH . I 7 HOH A 33 365 365 HOH HOH . I 7 HOH A 34 366 366 HOH HOH . I 7 HOH A 35 367 367 HOH HOH . I 7 HOH A 36 369 369 HOH HOH . I 7 HOH A 37 370 370 HOH HOH . I 7 HOH A 38 371 371 HOH HOH . I 7 HOH A 39 372 372 HOH HOH . I 7 HOH A 40 373 373 HOH HOH . I 7 HOH A 41 374 374 HOH HOH . I 7 HOH A 42 375 375 HOH HOH . I 7 HOH A 43 376 376 HOH HOH . I 7 HOH A 44 377 377 HOH HOH . I 7 HOH A 45 378 378 HOH HOH . I 7 HOH A 46 379 379 HOH HOH . I 7 HOH A 47 380 380 HOH HOH . I 7 HOH A 48 381 381 HOH HOH . I 7 HOH A 49 382 382 HOH HOH . I 7 HOH A 50 383 383 HOH HOH . I 7 HOH A 51 384 384 HOH HOH . I 7 HOH A 52 385 385 HOH HOH . I 7 HOH A 53 386 386 HOH HOH . I 7 HOH A 54 387 387 HOH HOH . I 7 HOH A 55 388 388 HOH HOH . I 7 HOH A 56 390 390 HOH HOH . I 7 HOH A 57 391 391 HOH HOH . I 7 HOH A 58 392 392 HOH HOH . I 7 HOH A 59 393 393 HOH HOH . I 7 HOH A 60 394 394 HOH HOH . I 7 HOH A 61 396 396 HOH HOH . I 7 HOH A 62 397 397 HOH HOH . I 7 HOH A 63 398 398 HOH HOH . I 7 HOH A 64 400 400 HOH HOH . I 7 HOH A 65 401 401 HOH HOH . I 7 HOH A 66 402 402 HOH HOH . I 7 HOH A 67 403 403 HOH HOH . I 7 HOH A 68 404 404 HOH HOH . I 7 HOH A 69 405 405 HOH HOH . I 7 HOH A 70 406 406 HOH HOH . I 7 HOH A 71 407 407 HOH HOH . I 7 HOH A 72 408 408 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 N N1 DCZ . . . E 5 -18.75 37.824 83.908 1 21.88 ? N1 DCZ 427 A 1 HETATM 2 C C2 DCZ . . . E 5 -18.024 36.715 83.461 1 21.32 ? C2 DCZ 427 A 1 HETATM 3 N N3 DCZ . . . E 5 -17.562 36.699 82.186 1 20.89 ? N3 DCZ 427 A 1 HETATM 4 C C4 DCZ . . . E 5 -17.838 37.721 81.361 1 22.01 ? C4 DCZ 427 A 1 HETATM 5 C C5 DCZ . . . E 5 -18.647 38.821 81.771 1 22.15 ? C5 DCZ 427 A 1 HETATM 6 C C6 DCZ . . . E 5 -19.079 38.83 83.04 1 22.11 ? C6 DCZ 427 A 1 HETATM 7 O O2 DCZ . . . E 5 -17.835 35.771 84.238 1 20.16 ? O2 DCZ 427 A 1 HETATM 8 N N4 DCZ . . . E 5 -17.321 37.696 80.127 1 22.2 ? N4 DCZ 427 A 1 HETATM 9 C C1' DCZ . . . E 5 -19.104 37.923 85.329 1 20.7 ? C1' DCZ 427 A 1 HETATM 10 C C2' DCZ . . . E 5 -17.871 37.742 86.212 1 20.33 ? C2' DCZ 427 A 1 HETATM 11 C C3' DCZ . . . E 5 -17.895 38.922 87.168 1 20.98 ? C3' DCZ 427 A 1 HETATM 12 C C4' DCZ . . . E 5 -18.665 39.99 86.386 1 19.79 ? C4' DCZ 427 A 1 HETATM 13 O O4' DCZ . . . E 5 -19.57 39.252 85.534 1 22.1 ? O4' DCZ 427 A 1 HETATM 14 O O3' DCZ . . . E 5 -18.473 38.445 88.379 1 17.15 ? O3' DCZ 427 A 1 HETATM 15 C C5' DCZ . . . E 5 -17.786 40.896 85.545 1 18 ? C5' DCZ 427 A 1 HETATM 16 O O5' DCZ . . . E 5 -18.42 41.746 84.587 1 9.14 ? O5' DCZ 427 A 1 # _model_server_stats.io_time_ms 67 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 16 #