data_1NJC # _model_server_result.job_id VALeOH8ppS8hBf55Hr8XRg _model_server_result.datetime_utc '2024-12-26 12:56:02' _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 1njc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":317}' # _entry.id 1NJC # _exptl.entry_id 1NJC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 307.197 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" _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 1NJC _cell.length_a 79.2 _cell.length_b 79.2 _cell.length_c 229.6 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1NJC _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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' 11_554 -x+y,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -114.8 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C9 H14 N3 O7 P' _chem_comp.formula_weight 307.197 _chem_comp.id DCM _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" _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 N1 C2 DCM sing 83 n n N1 C6 DCM sing 84 n n N1 C1' DCM sing 85 n n C2 N3 DCM sing 86 n n C2 O2 DCM doub 87 n n N3 C4 DCM doub 88 n n C4 C5 DCM sing 89 n n C4 N4 DCM sing 90 n n C5 C6 DCM doub 91 n n C5 H5 DCM sing 92 n n C6 H6 DCM sing 93 n n N4 HN41 DCM sing 94 n n N4 HN42 DCM sing 95 n n C1' C2' DCM sing 96 n n C1' O4' DCM sing 97 n n C1' H1' DCM sing 98 n n C2' C3' DCM sing 99 n n C2' "H2'1" DCM sing 100 n n C2' "H2'2" DCM sing 101 n n C3' C4' DCM sing 102 n n C3' O3' DCM sing 103 n n C3' H3' DCM sing 104 n n C4' O4' DCM sing 105 n n C4' C5' DCM sing 106 n n C4' H4' DCM sing 107 n n O3' HO3' DCM sing 108 n n C5' O5' DCM sing 109 n n C5' "H5'1" DCM sing 110 n n C5' "H5'2" DCM sing 111 n n O5' P DCM sing 112 n n P O1P DCM doub 113 n n P O2P DCM sing 114 n n P O3P DCM sing 115 n n O2P HOP2 DCM sing 116 n n O3P HOP3 DCM sing 117 n n # _atom_sites.entry_id 1NJC _atom_sites.fract_transf_matrix[1][1] 0.012626 _atom_sites.fract_transf_matrix[1][2] 0.00729 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01458 _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] 0.004355 _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 B 2 DCM A 1 317 317 DCM DCM . C 3 HOH A 1 318 318 HOH HOH . C 3 HOH A 2 319 319 HOH HOH . C 3 HOH A 3 320 320 HOH HOH . C 3 HOH A 4 321 321 HOH HOH . C 3 HOH A 5 322 322 HOH HOH . C 3 HOH A 6 323 323 HOH HOH . C 3 HOH A 7 324 324 HOH HOH . C 3 HOH A 8 325 325 HOH HOH . C 3 HOH A 9 326 326 HOH HOH . C 3 HOH A 10 327 327 HOH HOH . C 3 HOH A 11 328 328 HOH HOH . C 3 HOH A 12 329 329 HOH HOH . C 3 HOH A 13 330 330 HOH HOH . C 3 HOH A 14 331 331 HOH HOH . C 3 HOH A 15 332 332 HOH HOH . C 3 HOH A 16 333 333 HOH HOH . C 3 HOH A 17 334 334 HOH HOH . C 3 HOH A 18 335 335 HOH HOH . C 3 HOH A 19 336 336 HOH HOH . C 3 HOH A 20 337 337 HOH HOH . C 3 HOH A 21 338 338 HOH HOH . C 3 HOH A 22 339 339 HOH HOH . C 3 HOH A 23 340 340 HOH HOH . C 3 HOH A 24 341 341 HOH HOH . C 3 HOH A 25 342 342 HOH HOH . C 3 HOH A 26 343 343 HOH HOH . C 3 HOH A 27 344 344 HOH HOH . C 3 HOH A 28 345 345 HOH HOH . C 3 HOH A 29 346 346 HOH HOH . C 3 HOH A 30 347 347 HOH HOH . C 3 HOH A 31 348 348 HOH HOH . C 3 HOH A 32 349 349 HOH HOH . C 3 HOH A 33 350 350 HOH HOH . C 3 HOH A 34 351 351 HOH HOH . C 3 HOH A 35 352 352 HOH HOH . C 3 HOH A 36 353 353 HOH HOH . C 3 HOH A 37 354 354 HOH HOH . C 3 HOH A 38 355 355 HOH HOH . C 3 HOH A 39 356 356 HOH HOH . C 3 HOH A 40 357 357 HOH HOH . C 3 HOH A 41 358 358 HOH HOH . C 3 HOH A 42 359 359 HOH HOH . C 3 HOH A 43 360 360 HOH HOH . C 3 HOH A 44 361 361 HOH HOH . C 3 HOH A 45 362 362 HOH HOH . C 3 HOH A 46 363 363 HOH HOH . C 3 HOH A 47 364 364 HOH HOH . C 3 HOH A 48 365 365 HOH HOH . C 3 HOH A 49 366 366 HOH HOH . C 3 HOH A 50 367 367 HOH HOH . C 3 HOH A 51 368 368 HOH HOH . C 3 HOH A 52 369 369 HOH HOH . C 3 HOH A 53 370 370 HOH HOH . C 3 HOH A 54 371 371 HOH HOH . C 3 HOH A 55 372 372 HOH HOH . C 3 HOH A 56 373 373 HOH HOH . C 3 HOH A 57 374 374 HOH HOH . C 3 HOH A 58 375 375 HOH HOH . C 3 HOH A 59 376 376 HOH HOH . C 3 HOH A 60 377 377 HOH HOH . C 3 HOH A 61 379 379 HOH HOH . C 3 HOH A 62 380 380 HOH HOH . C 3 HOH A 63 381 381 HOH HOH . C 3 HOH A 64 382 382 HOH HOH . C 3 HOH A 65 383 383 HOH HOH . C 3 HOH A 66 384 384 HOH HOH . C 3 HOH A 67 385 385 HOH HOH . C 3 HOH A 68 386 386 HOH HOH . C 3 HOH A 69 387 387 HOH HOH . C 3 HOH A 70 388 388 HOH HOH . C 3 HOH A 71 390 390 HOH HOH . C 3 HOH A 72 391 391 HOH HOH . C 3 HOH A 73 392 392 HOH HOH . C 3 HOH A 74 393 393 HOH HOH . C 3 HOH A 75 394 394 HOH HOH . C 3 HOH A 76 395 395 HOH HOH . C 3 HOH A 77 396 396 HOH HOH . C 3 HOH A 78 397 397 HOH HOH . C 3 HOH A 79 399 399 HOH HOH . C 3 HOH A 80 400 400 HOH HOH . C 3 HOH A 81 401 401 HOH HOH . C 3 HOH A 82 402 402 HOH HOH . C 3 HOH A 83 403 403 HOH HOH . C 3 HOH A 84 404 404 HOH HOH . C 3 HOH A 85 407 407 HOH HOH . C 3 HOH A 86 408 408 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 DCM . . . B 2 14.902 46.438 -51.719 1 40 ? N1 DCM 317 A 1 HETATM 2 C C2 DCM . . . B 2 14.185 45.358 -51.225 1 41.45 ? C2 DCM 317 A 1 HETATM 3 N N3 DCM . . . B 2 13.711 45.409 -49.924 1 48.46 ? N3 DCM 317 A 1 HETATM 4 C C4 DCM . . . B 2 13.952 46.479 -49.126 1 51.67 ? C4 DCM 317 A 1 HETATM 5 C C5 DCM . . . B 2 14.664 47.615 -49.675 1 50.93 ? C5 DCM 317 A 1 HETATM 6 C C6 DCM . . . B 2 15.111 47.524 -51.002 1 46.51 ? C6 DCM 317 A 1 HETATM 7 O O2 DCM . . . B 2 13.943 44.346 -51.867 1 39.36 ? O2 DCM 317 A 1 HETATM 8 N N4 DCM . . . B 2 13.675 46.408 -47.821 1 52.1 ? N4 DCM 317 A 1 HETATM 9 C C1' DCM . . . B 2 15.721 46.337 -52.935 1 43.11 ? C1' DCM 317 A 1 HETATM 10 C C2' DCM . . . B 2 15.044 46.105 -54.288 1 40.58 ? C2' DCM 317 A 1 HETATM 11 C C3' DCM . . . B 2 16.232 46.225 -55.234 1 39.75 ? C3' DCM 317 A 1 HETATM 12 C C4' DCM . . . B 2 16.986 47.48 -54.813 1 40.37 ? C4' DCM 317 A 1 HETATM 13 O O4' DCM . . . B 2 16.624 47.473 -53.339 1 44.61 ? O4' DCM 317 A 1 HETATM 14 O O3' DCM . . . B 2 17.124 45.152 -54.91 1 34.54 ? O3' DCM 317 A 1 HETATM 15 C C5' DCM . . . B 2 16.408 48.712 -55.51 1 40.63 ? C5' DCM 317 A 1 HETATM 16 O O5' DCM . . . B 2 16.84 48.706 -56.907 1 38.07 ? O5' DCM 317 A 1 HETATM 17 P P DCM . . . B 2 15.963 49.419 -58 1 31.22 ? P DCM 317 A 1 HETATM 18 O O1P DCM . . . B 2 16.641 49.605 -59.308 1 32.3 ? O1P DCM 317 A 1 HETATM 19 O O2P DCM . . . B 2 14.904 48.406 -58.076 1 31.84 ? O2P DCM 317 A 1 HETATM 20 O O3P DCM . . . B 2 15.433 50.722 -57.586 1 31.31 ? O3P DCM 317 A 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 331 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 20 #