data_4JEM
#
_model_server_result.job_id            rni-PkOWgJ5smaRma9U09Q 
_model_server_result.datetime_utc      '2024-11-13 06:06:43' 
_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          4jem 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":201}' 
#
_entry.id    4JEM 
#
_exptl.entry_id    4JEM 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              323.197 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            "CYTIDINE-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          99.63 
_cell.angle_gamma         90 
_cell.entry_id            4JEM 
_cell.length_a            45.157 
_cell.length_b            100.386 
_cell.length_c            71.348 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4JEM 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        PISA 
_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,D,E,F 
_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 C N N 
? 2 D N N 
#
_chem_comp.formula           'C9 H14 N3 O8 P' 
_chem_comp.formula_weight    323.197 
_chem_comp.id                C5P 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              "CYTIDINE-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
O3P P C5P sing 70 n n 
O3P HOP3 C5P sing 71 n n 
P O1P C5P doub 72 n n 
P O2P C5P sing 73 n n 
P O5' C5P sing 74 n n 
O2P HOP2 C5P sing 75 n n 
O5' C5' C5P sing 76 n n 
C5' C4' C5P sing 77 n n 
C5' "H5'1" C5P sing 78 n n 
C5' "H5'2" C5P sing 79 n n 
C4' O4' C5P sing 80 n n 
C4' C3' C5P sing 81 n n 
C4' H4' C5P sing 82 n n 
O4' C1' C5P sing 83 n n 
C3' O3' C5P sing 84 n n 
C3' C2' C5P sing 85 n n 
C3' H3' C5P sing 86 n n 
O3' HO3' C5P sing 87 n n 
C2' O2' C5P sing 88 n n 
C2' C1' C5P sing 89 n n 
C2' "H2'1" C5P sing 90 n n 
O2' HO2' C5P sing 91 n n 
C1' N1 C5P sing 92 n n 
C1' H1' C5P sing 93 n n 
N1 C2 C5P sing 94 n n 
N1 C6 C5P sing 95 n n 
C2 N3 C5P sing 96 n n 
C2 O2 C5P doub 97 n n 
N3 C4 C5P doub 98 n n 
C4 C5 C5P sing 99 n n 
C4 N4 C5P sing 100 n n 
C5 C6 C5P doub 101 n n 
C5 H5 C5P sing 102 n n 
C6 H6 C5P sing 103 n n 
N4 HN41 C5P sing 104 n n 
N4 HN42 C5P sing 105 n n 
#
_atom_sites.entry_id                     4JEM 
_atom_sites.fract_transf_matrix[1][1]    0.022145 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.003756 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.009962 
_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]    0.014216 
_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 C5P A 1 201 1 C5P C5P . 
D 2 C5P B 1 201 1 C5P C5P . 
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 7 HOH HOH . 
E 3 HOH A 6 306 8 HOH HOH . 
E 3 HOH A 7 307 9 HOH HOH . 
E 3 HOH A 8 308 12 HOH HOH . 
E 3 HOH A 9 309 13 HOH HOH . 
E 3 HOH A 10 310 16 HOH HOH . 
E 3 HOH A 11 311 18 HOH HOH . 
E 3 HOH A 12 312 19 HOH HOH . 
E 3 HOH A 13 313 20 HOH HOH . 
E 3 HOH A 14 314 26 HOH HOH . 
E 3 HOH A 15 315 27 HOH HOH . 
E 3 HOH A 16 316 29 HOH HOH . 
E 3 HOH A 17 317 31 HOH HOH . 
E 3 HOH A 18 318 32 HOH HOH . 
E 3 HOH A 19 319 34 HOH HOH . 
E 3 HOH A 20 320 38 HOH HOH . 
E 3 HOH A 21 321 40 HOH HOH . 
E 3 HOH A 22 322 41 HOH HOH . 
E 3 HOH A 23 323 43 HOH HOH . 
E 3 HOH A 24 324 44 HOH HOH . 
E 3 HOH A 25 325 45 HOH HOH . 
E 3 HOH A 26 326 50 HOH HOH . 
E 3 HOH A 27 327 51 HOH HOH . 
E 3 HOH A 28 328 53 HOH HOH . 
E 3 HOH A 29 329 55 HOH HOH . 
E 3 HOH A 30 330 56 HOH HOH . 
E 3 HOH A 31 331 58 HOH HOH . 
E 3 HOH A 32 332 59 HOH HOH . 
E 3 HOH A 33 333 61 HOH HOH . 
E 3 HOH A 34 334 65 HOH HOH . 
E 3 HOH A 35 335 66 HOH HOH . 
E 3 HOH A 36 336 70 HOH HOH . 
E 3 HOH A 37 337 71 HOH HOH . 
E 3 HOH A 38 338 75 HOH HOH . 
E 3 HOH A 39 339 76 HOH HOH . 
E 3 HOH A 40 340 77 HOH HOH . 
E 3 HOH A 41 341 78 HOH HOH . 
E 3 HOH A 42 342 79 HOH HOH . 
E 3 HOH A 43 343 80 HOH HOH . 
E 3 HOH A 44 344 82 HOH HOH . 
E 3 HOH A 45 345 83 HOH HOH . 
E 3 HOH A 46 346 84 HOH HOH . 
E 3 HOH A 47 347 86 HOH HOH . 
E 3 HOH A 48 348 93 HOH HOH . 
E 3 HOH A 49 349 96 HOH HOH . 
E 3 HOH A 50 350 97 HOH HOH . 
E 3 HOH A 51 351 100 HOH HOH . 
E 3 HOH A 52 352 102 HOH HOH . 
E 3 HOH A 53 353 103 HOH HOH . 
E 3 HOH A 54 354 105 HOH HOH . 
E 3 HOH A 55 355 106 HOH HOH . 
E 3 HOH A 56 356 107 HOH HOH . 
E 3 HOH A 57 357 109 HOH HOH . 
E 3 HOH A 58 358 110 HOH HOH . 
E 3 HOH A 59 359 111 HOH HOH . 
E 3 HOH A 60 360 114 HOH HOH . 
E 3 HOH A 61 361 116 HOH HOH . 
E 3 HOH A 62 362 118 HOH HOH . 
E 3 HOH A 63 363 122 HOH HOH . 
E 3 HOH A 64 364 123 HOH HOH . 
E 3 HOH A 65 365 124 HOH HOH . 
E 3 HOH A 66 366 125 HOH HOH . 
E 3 HOH A 67 367 127 HOH HOH . 
E 3 HOH A 68 368 130 HOH HOH . 
E 3 HOH A 69 369 136 HOH HOH . 
E 3 HOH A 70 370 137 HOH HOH . 
E 3 HOH A 71 371 138 HOH HOH . 
E 3 HOH A 72 372 139 HOH HOH . 
E 3 HOH A 73 373 140 HOH HOH . 
E 3 HOH A 74 374 142 HOH HOH . 
E 3 HOH A 75 375 143 HOH HOH . 
E 3 HOH A 76 376 150 HOH HOH . 
E 3 HOH A 77 377 152 HOH HOH . 
E 3 HOH A 78 378 153 HOH HOH . 
E 3 HOH A 79 379 155 HOH HOH . 
E 3 HOH A 80 380 156 HOH HOH . 
E 3 HOH A 81 381 158 HOH HOH . 
E 3 HOH A 82 382 160 HOH HOH . 
E 3 HOH A 83 383 161 HOH HOH . 
E 3 HOH A 84 384 163 HOH HOH . 
E 3 HOH A 85 385 165 HOH HOH . 
E 3 HOH A 86 386 169 HOH HOH . 
E 3 HOH A 87 387 171 HOH HOH . 
E 3 HOH A 88 388 175 HOH HOH . 
E 3 HOH A 89 389 176 HOH HOH . 
E 3 HOH A 90 390 178 HOH HOH . 
E 3 HOH A 91 391 184 HOH HOH . 
E 3 HOH A 92 392 203 HOH HOH . 
E 3 HOH A 93 393 250 HOH HOH . 
E 3 HOH A 94 394 253 HOH HOH . 
E 3 HOH A 95 395 255 HOH HOH . 
E 3 HOH A 96 396 258 HOH HOH . 
E 3 HOH A 97 397 259 HOH HOH . 
E 3 HOH A 98 398 260 HOH HOH . 
E 3 HOH A 99 399 262 HOH HOH . 
E 3 HOH A 100 400 270 HOH HOH . 
F 3 HOH B 1 301 5 HOH HOH . 
F 3 HOH B 2 302 6 HOH HOH . 
F 3 HOH B 3 303 10 HOH HOH . 
F 3 HOH B 4 304 11 HOH HOH . 
F 3 HOH B 5 305 14 HOH HOH . 
F 3 HOH B 6 306 15 HOH HOH . 
F 3 HOH B 7 307 17 HOH HOH . 
F 3 HOH B 8 308 21 HOH HOH . 
F 3 HOH B 9 309 22 HOH HOH . 
F 3 HOH B 10 310 23 HOH HOH . 
F 3 HOH B 11 311 24 HOH HOH . 
F 3 HOH B 12 312 25 HOH HOH . 
F 3 HOH B 13 313 28 HOH HOH . 
F 3 HOH B 14 314 30 HOH HOH . 
F 3 HOH B 15 315 33 HOH HOH . 
F 3 HOH B 16 316 35 HOH HOH . 
F 3 HOH B 17 317 36 HOH HOH . 
F 3 HOH B 18 318 37 HOH HOH . 
F 3 HOH B 19 319 39 HOH HOH . 
F 3 HOH B 20 320 42 HOH HOH . 
F 3 HOH B 21 321 46 HOH HOH . 
F 3 HOH B 22 322 47 HOH HOH . 
F 3 HOH B 23 323 48 HOH HOH . 
F 3 HOH B 24 324 49 HOH HOH . 
F 3 HOH B 25 325 52 HOH HOH . 
F 3 HOH B 26 326 54 HOH HOH . 
F 3 HOH B 27 327 57 HOH HOH . 
F 3 HOH B 28 328 60 HOH HOH . 
F 3 HOH B 29 329 62 HOH HOH . 
F 3 HOH B 30 330 63 HOH HOH . 
F 3 HOH B 31 331 64 HOH HOH . 
F 3 HOH B 32 332 67 HOH HOH . 
F 3 HOH B 33 333 68 HOH HOH . 
F 3 HOH B 34 334 69 HOH HOH . 
F 3 HOH B 35 335 72 HOH HOH . 
F 3 HOH B 36 336 73 HOH HOH . 
F 3 HOH B 37 337 74 HOH HOH . 
F 3 HOH B 38 338 81 HOH HOH . 
F 3 HOH B 39 339 85 HOH HOH . 
F 3 HOH B 40 340 87 HOH HOH . 
F 3 HOH B 41 341 88 HOH HOH . 
F 3 HOH B 42 342 89 HOH HOH . 
F 3 HOH B 43 343 90 HOH HOH . 
F 3 HOH B 44 344 91 HOH HOH . 
F 3 HOH B 45 345 92 HOH HOH . 
F 3 HOH B 46 346 94 HOH HOH . 
F 3 HOH B 47 347 95 HOH HOH . 
F 3 HOH B 48 348 98 HOH HOH . 
F 3 HOH B 49 349 99 HOH HOH . 
F 3 HOH B 50 350 101 HOH HOH . 
F 3 HOH B 51 351 104 HOH HOH . 
F 3 HOH B 52 352 108 HOH HOH . 
F 3 HOH B 53 353 113 HOH HOH . 
F 3 HOH B 54 354 115 HOH HOH . 
F 3 HOH B 55 355 117 HOH HOH . 
F 3 HOH B 56 356 119 HOH HOH . 
F 3 HOH B 57 357 120 HOH HOH . 
F 3 HOH B 58 358 121 HOH HOH . 
F 3 HOH B 59 359 126 HOH HOH . 
F 3 HOH B 60 360 128 HOH HOH . 
F 3 HOH B 61 361 129 HOH HOH . 
F 3 HOH B 62 362 131 HOH HOH . 
F 3 HOH B 63 363 132 HOH HOH . 
F 3 HOH B 64 364 133 HOH HOH . 
F 3 HOH B 65 365 135 HOH HOH . 
F 3 HOH B 66 366 141 HOH HOH . 
F 3 HOH B 67 367 145 HOH HOH . 
F 3 HOH B 68 368 146 HOH HOH . 
F 3 HOH B 69 369 147 HOH HOH . 
F 3 HOH B 70 370 148 HOH HOH . 
F 3 HOH B 71 371 151 HOH HOH . 
F 3 HOH B 72 372 154 HOH HOH . 
F 3 HOH B 73 373 157 HOH HOH . 
F 3 HOH B 74 374 159 HOH HOH . 
F 3 HOH B 75 375 162 HOH HOH . 
F 3 HOH B 76 376 166 HOH HOH . 
F 3 HOH B 77 377 167 HOH HOH . 
F 3 HOH B 78 378 168 HOH HOH . 
F 3 HOH B 79 379 174 HOH HOH . 
F 3 HOH B 80 380 181 HOH HOH . 
F 3 HOH B 81 381 182 HOH HOH . 
F 3 HOH B 82 382 183 HOH HOH . 
F 3 HOH B 83 383 192 HOH HOH . 
F 3 HOH B 84 384 249 HOH HOH . 
F 3 HOH B 85 385 251 HOH HOH . 
F 3 HOH B 86 386 252 HOH HOH . 
F 3 HOH B 87 387 256 HOH HOH . 
F 3 HOH B 88 388 261 HOH HOH . 
F 3 HOH B 89 389 264 HOH HOH . 
F 3 HOH B 90 390 265 HOH HOH . 
F 3 HOH B 91 391 267 HOH HOH . 
F 3 HOH B 92 392 268 HOH HOH . 
F 3 HOH B 93 393 269 HOH HOH . 
F 3 HOH B 94 394 279 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 O3P C5P . . . D 2 13.592 17.851 20.621 1 15.7 ? O3P C5P 201 B 1 
HETATM 2 P P C5P . . . D 2 13.573 19.365 20.364 1 13.13 ? P C5P 201 B 1 
HETATM 3 O O1P C5P . . . D 2 14.468 20.121 21.301 1 13.13 ? O1P C5P 201 B 1 
HETATM 4 O O2P C5P . . . D 2 13.766 19.664 18.877 1 13.84 ? O2P C5P 201 B 1 
HETATM 5 O O5' C5P . . . D 2 12.062 19.763 20.691 1 12.71 ? O5' C5P 201 B 1 
HETATM 6 C C5' C5P . . . D 2 11.668 21.118 20.634 1 13.86 ? C5' C5P 201 B 1 
HETATM 7 C C4' C5P . . . D 2 10.218 21.303 20.98 1 13.45 ? C4' C5P 201 B 1 
HETATM 8 O O4' C5P . . . D 2 9.929 20.735 22.285 1 16.1 ? O4' C5P 201 B 1 
HETATM 9 C C3' C5P . . . D 2 9.742 22.759 21.038 1 11.72 ? C3' C5P 201 B 1 
HETATM 10 O O3' C5P . . . D 2 8.623 22.982 20.201 1 11.98 ? O3' C5P 201 B 1 
HETATM 11 C C2' C5P . . . D 2 9.51 23.07 22.532 1 14.93 ? C2' C5P 201 B 1 
HETATM 12 O O2' C5P . . . D 2 8.15 23.427 22.783 1 15.39 ? O2' C5P 201 B 1 
HETATM 13 C C1' C5P . . . D 2 9.835 21.748 23.254 1 15.41 ? C1' C5P 201 B 1 
HETATM 14 N N1 C5P . . . D 2 11.125 21.813 24.002 1 17.46 ? N1 C5P 201 B 1 
HETATM 15 C C2 C5P . . . D 2 11.105 22.776 25.116 1 16.68 ? C2 C5P 201 B 1 
HETATM 16 N N3 C5P . . . D 2 12.263 22.98 25.932 1 18.91 ? N3 C5P 201 B 1 
HETATM 17 C C4 C5P . . . D 2 13.468 22.259 25.7 1 20.41 ? C4 C5P 201 B 1 
HETATM 18 C C5 C5P . . . D 2 13.532 21.291 24.606 1 21.52 ? C5 C5P 201 B 1 
HETATM 19 C C6 C5P . . . D 2 12.342 21.09 23.778 1 18.72 ? C6 C5P 201 B 1 
HETATM 20 O O2 C5P . . . D 2 10.132 23.435 25.443 1 19.09 ? O2 C5P 201 B 1 
HETATM 21 N N4 C5P . . . D 2 14.595 22.499 26.52 1 24.79 ? N4 C5P 201 B 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           230 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           21 
#