data_1B5D # _model_server_result.job_id 8GTe-xHQHk6-1jrHeqPBZA _model_server_result.datetime_utc '2024-10-12 00:14:55' _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 1b5d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":400}' # _entry.id 1B5D # _exptl.entry_id 1B5D _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 115.54 _cell.angle_gamma 90 _cell.entry_id 1B5D _cell.length_a 176.23 _cell.length_b 53.29 _cell.length_c 75.86 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1B5D _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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 ? tetrameric 4 author_defined_assembly 1 PISA,PQS dimeric 2 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,B,C,D,E,F 1 1,2 A,B,C,D,E,F 2 1 # 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' 4_556 -x+1/2,y+1/2,-z+1 -1 0 0 0 1 0 0 0 -1 55.408635 26.645 68.447303 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 D N 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 1B5D _atom_sites.fract_transf_matrix[1][1] 0.005674 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002711 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018765 _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] 0.01461 _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 C 2 DCM A 1 300 300 DCM CMP . D 2 DCM B 1 400 300 DCM CMP . E 3 HOH A 1 301 1 HOH HOH . E 3 HOH A 2 302 2 HOH HOH . E 3 HOH A 3 303 3 HOH HOH . E 3 HOH A 4 304 4 HOH HOH . E 3 HOH A 5 305 5 HOH HOH . E 3 HOH A 6 306 6 HOH HOH . E 3 HOH A 7 307 7 HOH HOH . E 3 HOH A 8 308 8 HOH HOH . E 3 HOH A 9 309 9 HOH HOH . E 3 HOH A 10 310 10 HOH HOH . E 3 HOH A 11 311 11 HOH HOH . E 3 HOH A 12 312 12 HOH HOH . E 3 HOH A 13 313 13 HOH HOH . E 3 HOH A 14 314 14 HOH HOH . E 3 HOH A 15 315 15 HOH HOH . E 3 HOH A 16 316 16 HOH HOH . E 3 HOH A 17 317 17 HOH HOH . E 3 HOH A 18 318 18 HOH HOH . E 3 HOH A 19 319 19 HOH HOH . E 3 HOH A 20 320 20 HOH HOH . E 3 HOH A 21 321 21 HOH HOH . E 3 HOH A 22 322 22 HOH HOH . E 3 HOH A 23 323 45 HOH HOH . E 3 HOH A 24 324 46 HOH HOH . E 3 HOH A 25 325 47 HOH HOH . E 3 HOH A 26 326 48 HOH HOH . E 3 HOH A 27 327 49 HOH HOH . E 3 HOH A 28 328 50 HOH HOH . E 3 HOH A 29 329 51 HOH HOH . E 3 HOH A 30 330 52 HOH HOH . E 3 HOH A 31 331 53 HOH HOH . E 3 HOH A 32 332 54 HOH HOH . E 3 HOH A 33 333 55 HOH HOH . E 3 HOH A 34 334 56 HOH HOH . E 3 HOH A 35 335 57 HOH HOH . E 3 HOH A 36 336 58 HOH HOH . E 3 HOH A 37 337 59 HOH HOH . E 3 HOH A 38 338 60 HOH HOH . E 3 HOH A 39 339 63 HOH HOH . E 3 HOH A 40 340 64 HOH HOH . E 3 HOH A 41 341 65 HOH HOH . E 3 HOH A 42 342 66 HOH HOH . E 3 HOH A 43 343 67 HOH HOH . E 3 HOH A 44 344 68 HOH HOH . E 3 HOH A 45 345 69 HOH HOH . E 3 HOH A 46 346 70 HOH HOH . E 3 HOH A 47 347 71 HOH HOH . E 3 HOH A 48 348 72 HOH HOH . E 3 HOH A 49 349 74 HOH HOH . E 3 HOH A 50 350 99 HOH HOH . E 3 HOH A 51 351 100 HOH HOH . E 3 HOH A 52 352 101 HOH HOH . E 3 HOH A 53 353 102 HOH HOH . E 3 HOH A 54 354 103 HOH HOH . E 3 HOH A 55 355 104 HOH HOH . E 3 HOH A 56 356 105 HOH HOH . E 3 HOH A 57 357 106 HOH HOH . E 3 HOH A 58 358 107 HOH HOH . E 3 HOH A 59 359 108 HOH HOH . E 3 HOH A 60 360 109 HOH HOH . E 3 HOH A 61 361 110 HOH HOH . E 3 HOH A 62 362 122 HOH HOH . E 3 HOH A 63 363 123 HOH HOH . E 3 HOH A 64 364 129 HOH HOH . E 3 HOH A 65 365 131 HOH HOH . E 3 HOH A 66 366 134 HOH HOH . E 3 HOH A 67 367 135 HOH HOH . E 3 HOH A 68 368 136 HOH HOH . E 3 HOH A 69 369 138 HOH HOH . E 3 HOH A 70 370 139 HOH HOH . E 3 HOH A 71 371 140 HOH HOH . E 3 HOH A 72 372 141 HOH HOH . E 3 HOH A 73 373 142 HOH HOH . E 3 HOH A 74 374 147 HOH HOH . E 3 HOH A 75 375 148 HOH HOH . E 3 HOH A 76 376 149 HOH HOH . E 3 HOH A 77 377 151 HOH HOH . F 3 HOH B 1 401 23 HOH HOH . F 3 HOH B 2 402 24 HOH HOH . F 3 HOH B 3 403 25 HOH HOH . F 3 HOH B 4 404 26 HOH HOH . F 3 HOH B 5 405 27 HOH HOH . F 3 HOH B 6 406 28 HOH HOH . F 3 HOH B 7 407 29 HOH HOH . F 3 HOH B 8 408 30 HOH HOH . F 3 HOH B 9 409 31 HOH HOH . F 3 HOH B 10 410 32 HOH HOH . F 3 HOH B 11 411 33 HOH HOH . F 3 HOH B 12 412 34 HOH HOH . F 3 HOH B 13 413 35 HOH HOH . F 3 HOH B 14 414 36 HOH HOH . F 3 HOH B 15 415 37 HOH HOH . F 3 HOH B 16 416 38 HOH HOH . F 3 HOH B 17 417 39 HOH HOH . F 3 HOH B 18 418 40 HOH HOH . F 3 HOH B 19 419 41 HOH HOH . F 3 HOH B 20 420 42 HOH HOH . F 3 HOH B 21 421 43 HOH HOH . F 3 HOH B 22 422 44 HOH HOH . F 3 HOH B 23 423 61 HOH HOH . F 3 HOH B 24 424 62 HOH HOH . F 3 HOH B 25 425 73 HOH HOH . F 3 HOH B 26 426 75 HOH HOH . F 3 HOH B 27 427 76 HOH HOH . F 3 HOH B 28 428 77 HOH HOH . F 3 HOH B 29 429 78 HOH HOH . F 3 HOH B 30 430 79 HOH HOH . F 3 HOH B 31 431 80 HOH HOH . F 3 HOH B 32 432 81 HOH HOH . F 3 HOH B 33 433 82 HOH HOH . F 3 HOH B 34 434 83 HOH HOH . F 3 HOH B 35 435 84 HOH HOH . F 3 HOH B 36 436 85 HOH HOH . F 3 HOH B 37 437 86 HOH HOH . F 3 HOH B 38 438 87 HOH HOH . F 3 HOH B 39 439 88 HOH HOH . F 3 HOH B 40 440 89 HOH HOH . F 3 HOH B 41 441 90 HOH HOH . F 3 HOH B 42 442 91 HOH HOH . F 3 HOH B 43 443 92 HOH HOH . F 3 HOH B 44 444 93 HOH HOH . F 3 HOH B 45 445 94 HOH HOH . F 3 HOH B 46 446 95 HOH HOH . F 3 HOH B 47 447 96 HOH HOH . F 3 HOH B 48 448 97 HOH HOH . F 3 HOH B 49 449 98 HOH HOH . F 3 HOH B 50 450 111 HOH HOH . F 3 HOH B 51 451 112 HOH HOH . F 3 HOH B 52 452 113 HOH HOH . F 3 HOH B 53 453 114 HOH HOH . F 3 HOH B 54 454 115 HOH HOH . F 3 HOH B 55 455 116 HOH HOH . F 3 HOH B 56 456 117 HOH HOH . F 3 HOH B 57 457 118 HOH HOH . F 3 HOH B 58 458 119 HOH HOH . F 3 HOH B 59 459 120 HOH HOH . F 3 HOH B 60 460 121 HOH HOH . F 3 HOH B 61 461 124 HOH HOH . F 3 HOH B 62 462 125 HOH HOH . F 3 HOH B 63 463 126 HOH HOH . F 3 HOH B 64 464 127 HOH HOH . F 3 HOH B 65 465 128 HOH HOH . F 3 HOH B 66 466 130 HOH HOH . F 3 HOH B 67 467 132 HOH HOH . F 3 HOH B 68 468 133 HOH HOH . F 3 HOH B 69 469 137 HOH HOH . F 3 HOH B 70 470 143 HOH HOH . F 3 HOH B 71 471 144 HOH HOH . F 3 HOH B 72 472 145 HOH HOH . F 3 HOH B 73 473 146 HOH HOH . F 3 HOH B 74 474 150 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 . . . D 2 30.491 -0.773 -1.882 1 37.34 ? N1 DCM 400 B 1 HETATM 2 C C2 DCM . . . D 2 29.401 -1.652 -1.696 1 34.71 ? C2 DCM 400 B 1 HETATM 3 N N3 DCM . . . D 2 29.52 -2.669 -0.824 1 35.61 ? N3 DCM 400 B 1 HETATM 4 C C4 DCM . . . D 2 30.713 -2.939 -0.267 1 43.27 ? C4 DCM 400 B 1 HETATM 5 C C5 DCM . . . D 2 31.831 -2.06 -0.419 1 41.46 ? C5 DCM 400 B 1 HETATM 6 C C6 DCM . . . D 2 31.667 -0.983 -1.203 1 39.47 ? C6 DCM 400 B 1 HETATM 7 O O2 DCM . . . D 2 28.375 -1.491 -2.38 1 31.63 ? O2 DCM 400 B 1 HETATM 8 N N4 DCM . . . D 2 30.846 -4.08 0.42 1 33.74 ? N4 DCM 400 B 1 HETATM 9 C C1' DCM . . . D 2 30.389 0.297 -2.891 1 32.2 ? C1' DCM 400 B 1 HETATM 10 C C2' DCM . . . D 2 29.355 1.37 -2.546 1 28.84 ? C2' DCM 400 B 1 HETATM 11 C C3' DCM . . . D 2 29.914 2.575 -3.291 1 26.75 ? C3' DCM 400 B 1 HETATM 12 C C4' DCM . . . D 2 31.423 2.39 -3.162 1 30.48 ? C4' DCM 400 B 1 HETATM 13 O O4' DCM . . . D 2 31.636 0.964 -2.969 1 32.04 ? O4' DCM 400 B 1 HETATM 14 O O3' DCM . . . D 2 29.538 2.564 -4.66 1 25.45 ? O3' DCM 400 B 1 HETATM 15 C C5' DCM . . . D 2 32.078 3.165 -2.039 1 21.89 ? C5' DCM 400 B 1 HETATM 16 O O5' DCM . . . D 2 32.213 4.56 -2.41 1 24.76 ? O5' DCM 400 B 1 HETATM 17 P P DCM . . . D 2 31.972 5.736 -1.354 1 21.63 ? P DCM 400 B 1 HETATM 18 O O1P DCM . . . D 2 30.533 5.517 -1.023 1 22.21 ? O1P DCM 400 B 1 HETATM 19 O O2P DCM . . . D 2 32.965 5.379 -0.309 1 20.13 ? O2P DCM 400 B 1 HETATM 20 O O3P DCM . . . D 2 32.301 6.882 -2.237 1 21.19 ? O3P DCM 400 B 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 359 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 20 #