data_3RU7
#
_model_server_result.job_id            Fbxur-IESS096nquNKwpPQ 
_model_server_result.datetime_utc      '2025-02-05 09:48:32' 
_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          3ru7 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":349}' 
#
_entry.id    3RU7 
#
_exptl.entry_id    3RU7 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              663.425 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            NICOTINAMIDE-ADENINE-DINUCLEOTIDE 
_entity.pdbx_number_of_molecules    4 
_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            3RU7 
_cell.length_a            77.73 
_cell.length_b            77.73 
_cell.length_c            224.54 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3RU7 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        145 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 32' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_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,C,E,F,G,H,I,N,O,P,Q,U,W 1 1 
B,J,K,L,M,V 2 1 
D,R,S,T,X 2 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' 3_665 -x+y+1,-x+1,z+1/3 -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 38.865 67.316155 74.846667 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 E N N 
? 2 J N N 
? 2 N N N 
? 2 S N N 
#
_chem_comp.formula           'C21 H27 N7 O14 P2' 
_chem_comp.formula_weight    663.425 
_chem_comp.id                NAD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              NICOTINAMIDE-ADENINE-DINUCLEOTIDE 
_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 NAD doub 237 n n 
PA O2A NAD sing 238 n n 
PA O5B NAD sing 239 n n 
PA O3 NAD sing 240 n n 
O2A HOA2 NAD sing 241 n n 
O5B C5B NAD sing 242 n n 
C5B C4B NAD sing 243 n n 
C5B H51A NAD sing 244 n n 
C5B H52A NAD sing 245 n n 
C4B O4B NAD sing 246 n n 
C4B C3B NAD sing 247 n n 
C4B H4B NAD sing 248 n n 
O4B C1B NAD sing 249 n n 
C3B O3B NAD sing 250 n n 
C3B C2B NAD sing 251 n n 
C3B H3B NAD sing 252 n n 
O3B HO3A NAD sing 253 n n 
C2B O2B NAD sing 254 n n 
C2B C1B NAD sing 255 n n 
C2B H2B NAD sing 256 n n 
O2B HO2A NAD sing 257 n n 
C1B N9A NAD sing 258 n n 
C1B H1B NAD sing 259 n n 
N9A C8A NAD sing 260 n y 
N9A C4A NAD sing 261 n y 
C8A N7A NAD doub 262 n y 
C8A H8A NAD sing 263 n n 
N7A C5A NAD sing 264 n y 
C5A C6A NAD sing 265 n y 
C5A C4A NAD doub 266 n y 
C6A N6A NAD sing 267 n n 
C6A N1A NAD doub 268 n y 
N6A H61A NAD sing 269 n n 
N6A H62A NAD sing 270 n n 
N1A C2A NAD sing 271 n y 
C2A N3A NAD doub 272 n y 
C2A H2A NAD sing 273 n n 
N3A C4A NAD sing 274 n y 
O3 PN NAD sing 275 n n 
PN O1N NAD doub 276 n n 
PN O2N NAD sing 277 n n 
PN O5D NAD sing 278 n n 
O5D C5D NAD sing 279 n n 
C5D C4D NAD sing 280 n n 
C5D H51N NAD sing 281 n n 
C5D H52N NAD sing 282 n n 
C4D O4D NAD sing 283 n n 
C4D C3D NAD sing 284 n n 
C4D H4D NAD sing 285 n n 
O4D C1D NAD sing 286 n n 
C3D O3D NAD sing 287 n n 
C3D C2D NAD sing 288 n n 
C3D H3D NAD sing 289 n n 
O3D HO3N NAD sing 290 n n 
C2D O2D NAD sing 291 n n 
C2D C1D NAD sing 292 n n 
C2D H2D NAD sing 293 n n 
O2D HO2N NAD sing 294 n n 
C1D N1N NAD sing 295 n n 
C1D H1D NAD sing 296 n n 
N1N C2N NAD sing 297 n y 
N1N C6N NAD doub 298 n y 
C2N C3N NAD doub 299 n y 
C2N H2N NAD sing 300 n n 
C3N C7N NAD sing 301 n n 
C3N C4N NAD sing 302 n y 
C7N O7N NAD doub 303 n n 
C7N N7N NAD sing 304 n n 
N7N H71N NAD sing 305 n n 
N7N H72N NAD sing 306 n n 
C4N C5N NAD doub 307 n y 
C4N H4N NAD sing 308 n n 
C5N C6N NAD sing 309 n y 
C5N H5N NAD sing 310 n n 
C6N H6N NAD sing 311 n n 
#
_atom_sites.entry_id                     3RU7 
_atom_sites.fract_transf_matrix[1][1]    0.012865 
_atom_sites.fract_transf_matrix[1][2]    0.007428 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014855 
_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]    0.004454 
_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 2 NAD A 1 349 349 NAD NAD . 
F 3 GLY A 1 353 353 GLY GLY . 
G 4 NA A 1 351 351 NA NA . 
H 4 NA A 1 352 352 NA NA . 
I 5 UNL A 1 350 350 UNL UNL . 
J 2 NAD B 1 349 349 NAD NAD . 
K 5 UNL B 1 350 350 UNL UNL . 
L 4 NA B 1 351 351 NA NA . 
M 6 SO4 B 1 352 352 SO4 SO4 . 
N 2 NAD C 1 349 349 NAD NAD . 
O 5 UNL C 1 350 350 UNL UNL . 
P 6 SO4 C 1 351 351 SO4 SO4 . 
Q 4 NA C 1 352 352 NA NA . 
R 3 GLY D 1 351 351 GLY GLY . 
S 2 NAD D 1 349 349 NAD NAD . 
T 5 UNL D 1 350 350 UNL UNL . 
U 7 HOH A 1 354 354 HOH HOH . 
U 7 HOH A 2 355 355 HOH HOH . 
U 7 HOH A 3 356 356 HOH HOH . 
U 7 HOH A 4 357 357 HOH HOH . 
U 7 HOH A 5 358 358 HOH HOH . 
U 7 HOH A 6 359 359 HOH HOH . 
U 7 HOH A 7 360 360 HOH HOH . 
U 7 HOH A 8 361 361 HOH HOH . 
U 7 HOH A 9 362 362 HOH HOH . 
U 7 HOH A 10 363 363 HOH HOH . 
U 7 HOH A 11 364 364 HOH HOH . 
U 7 HOH A 12 365 365 HOH HOH . 
U 7 HOH A 13 366 366 HOH HOH . 
U 7 HOH A 14 367 367 HOH HOH . 
U 7 HOH A 15 368 368 HOH HOH . 
U 7 HOH A 16 369 369 HOH HOH . 
U 7 HOH A 17 370 370 HOH HOH . 
U 7 HOH A 18 371 371 HOH HOH . 
U 7 HOH A 19 372 372 HOH HOH . 
U 7 HOH A 20 373 373 HOH HOH . 
U 7 HOH A 21 374 374 HOH HOH . 
U 7 HOH A 22 375 375 HOH HOH . 
U 7 HOH A 23 376 376 HOH HOH . 
U 7 HOH A 24 377 377 HOH HOH . 
U 7 HOH A 25 378 378 HOH HOH . 
U 7 HOH A 26 379 379 HOH HOH . 
U 7 HOH A 27 380 380 HOH HOH . 
V 7 HOH B 1 353 353 HOH HOH . 
V 7 HOH B 2 354 354 HOH HOH . 
V 7 HOH B 3 355 355 HOH HOH . 
V 7 HOH B 4 356 356 HOH HOH . 
V 7 HOH B 5 357 357 HOH HOH . 
V 7 HOH B 6 358 358 HOH HOH . 
V 7 HOH B 7 359 359 HOH HOH . 
V 7 HOH B 8 360 360 HOH HOH . 
V 7 HOH B 9 361 361 HOH HOH . 
V 7 HOH B 10 362 362 HOH HOH . 
V 7 HOH B 11 363 363 HOH HOH . 
V 7 HOH B 12 364 364 HOH HOH . 
V 7 HOH B 13 365 365 HOH HOH . 
V 7 HOH B 14 366 366 HOH HOH . 
V 7 HOH B 15 367 367 HOH HOH . 
V 7 HOH B 16 368 368 HOH HOH . 
V 7 HOH B 17 369 369 HOH HOH . 
V 7 HOH B 18 370 370 HOH HOH . 
V 7 HOH B 19 371 371 HOH HOH . 
V 7 HOH B 20 372 372 HOH HOH . 
V 7 HOH B 21 373 373 HOH HOH . 
V 7 HOH B 22 374 374 HOH HOH . 
V 7 HOH B 23 375 375 HOH HOH . 
V 7 HOH B 24 376 376 HOH HOH . 
V 7 HOH B 25 377 377 HOH HOH . 
V 7 HOH B 26 378 378 HOH HOH . 
V 7 HOH B 27 379 379 HOH HOH . 
V 7 HOH B 28 380 380 HOH HOH . 
V 7 HOH B 29 381 381 HOH HOH . 
W 7 HOH C 1 353 353 HOH HOH . 
W 7 HOH C 2 354 354 HOH HOH . 
W 7 HOH C 3 355 355 HOH HOH . 
W 7 HOH C 4 356 356 HOH HOH . 
W 7 HOH C 5 357 357 HOH HOH . 
W 7 HOH C 6 358 358 HOH HOH . 
W 7 HOH C 7 359 359 HOH HOH . 
W 7 HOH C 8 360 360 HOH HOH . 
W 7 HOH C 9 361 361 HOH HOH . 
W 7 HOH C 10 362 362 HOH HOH . 
W 7 HOH C 11 363 363 HOH HOH . 
W 7 HOH C 12 364 364 HOH HOH . 
W 7 HOH C 13 365 365 HOH HOH . 
W 7 HOH C 14 366 366 HOH HOH . 
W 7 HOH C 15 367 367 HOH HOH . 
W 7 HOH C 16 368 368 HOH HOH . 
W 7 HOH C 17 369 369 HOH HOH . 
W 7 HOH C 18 370 370 HOH HOH . 
X 7 HOH D 1 352 352 HOH HOH . 
X 7 HOH D 2 353 353 HOH HOH . 
X 7 HOH D 3 354 354 HOH HOH . 
X 7 HOH D 4 355 355 HOH HOH . 
X 7 HOH D 5 356 356 HOH HOH . 
X 7 HOH D 6 357 357 HOH HOH . 
X 7 HOH D 7 358 358 HOH HOH . 
X 7 HOH D 8 359 359 HOH HOH . 
X 7 HOH D 9 360 360 HOH HOH . 
X 7 HOH D 10 361 361 HOH HOH . 
X 7 HOH D 11 362 362 HOH HOH . 
X 7 HOH D 12 363 363 HOH HOH . 
X 7 HOH D 13 364 364 HOH HOH . 
X 7 HOH D 14 365 365 HOH HOH . 
X 7 HOH D 15 366 366 HOH HOH . 
X 7 HOH D 16 367 367 HOH HOH . 
X 7 HOH D 17 368 368 HOH HOH . 
X 7 HOH D 18 369 369 HOH HOH . 
X 7 HOH D 19 370 370 HOH HOH . 
X 7 HOH D 20 371 371 HOH HOH . 
X 7 HOH D 21 372 372 HOH HOH . 
X 7 HOH D 22 373 373 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 NAD . . . J 2 7.436 15.909 13.02 1 26.28 ? PA NAD 349 B 1 
HETATM 2 O O1A NAD . . . J 2 7.346 15.511 11.594 1 26.13 ? O1A NAD 349 B 1 
HETATM 3 O O2A NAD . . . J 2 6.978 17.257 13.428 1 27.03 ? O2A NAD 349 B 1 
HETATM 4 O O5B NAD . . . J 2 6.676 14.787 13.881 1 26.73 ? O5B NAD 349 B 1 
HETATM 5 C C5B NAD . . . J 2 6.223 15.002 15.207 1 24.7 ? C5B NAD 349 B 1 
HETATM 6 C C4B NAD . . . J 2 4.826 14.433 15.32 1 26.22 ? C4B NAD 349 B 1 
HETATM 7 O O4B NAD . . . J 2 4.376 14.574 16.692 1 27.76 ? O4B NAD 349 B 1 
HETATM 8 C C3B NAD . . . J 2 3.86 15.273 14.454 1 27.79 ? C3B NAD 349 B 1 
HETATM 9 O O3B NAD . . . J 2 3.036 14.398 13.689 1 27.62 ? O3B NAD 349 B 1 
HETATM 10 C C2B NAD . . . J 2 3.015 16.051 15.467 1 28.3 ? C2B NAD 349 B 1 
HETATM 11 O O2B NAD . . . J 2 1.698 16.238 14.967 1 30.84 ? O2B NAD 349 B 1 
HETATM 12 C C1B NAD . . . J 2 3.007 15.096 16.66 1 28.3 ? C1B NAD 349 B 1 
HETATM 13 N N9A NAD . . . J 2 2.786 15.767 17.962 1 27.27 ? N9A NAD 349 B 1 
HETATM 14 C C8A NAD . . . J 2 3.453 16.828 18.416 1 25.92 ? C8A NAD 349 B 1 
HETATM 15 N N7A NAD . . . J 2 3.006 17.139 19.631 1 26.68 ? N7A NAD 349 B 1 
HETATM 16 C C5A NAD . . . J 2 2.054 16.271 19.959 1 27.06 ? C5A NAD 349 B 1 
HETATM 17 C C6A NAD . . . J 2 1.234 16.105 21.072 1 27.32 ? C6A NAD 349 B 1 
HETATM 18 N N6A NAD . . . J 2 1.315 16.925 22.107 1 25.98 ? N6A NAD 349 B 1 
HETATM 19 N N1A NAD . . . J 2 0.342 15.097 21.088 1 30.13 ? N1A NAD 349 B 1 
HETATM 20 C C2A NAD . . . J 2 0.236 14.264 20.052 1 31.35 ? C2A NAD 349 B 1 
HETATM 21 N N3A NAD . . . J 2 1.003 14.404 18.975 1 30.39 ? N3A NAD 349 B 1 
HETATM 22 C C4A NAD . . . J 2 1.917 15.392 18.897 1 28.14 ? C4A NAD 349 B 1 
HETATM 23 O O3 NAD . . . J 2 8.912 15.714 13.601 1 26.27 ? O3 NAD 349 B 1 
HETATM 24 P PN NAD . . . J 2 9.866 14.5 13.227 1 26.4 ? PN NAD 349 B 1 
HETATM 25 O O1N NAD . . . J 2 9.119 13.385 12.616 1 28.64 ? O1N NAD 349 B 1 
HETATM 26 O O2N NAD . . . J 2 10.973 15.108 12.476 1 29.29 ? O2N NAD 349 B 1 
HETATM 27 O O5D NAD . . . J 2 10.453 14.058 14.641 1 26.74 ? O5D NAD 349 B 1 
HETATM 28 C C5D NAD . . . J 2 9.854 13.077 15.495 1 26.75 ? C5D NAD 349 B 1 
HETATM 29 C C4D NAD . . . J 2 10.675 12.921 16.791 1 26.38 ? C4D NAD 349 B 1 
HETATM 30 O O4D NAD . . . J 2 12.102 12.882 16.502 1 26.62 ? O4D NAD 349 B 1 
HETATM 31 C C3D NAD . . . J 2 10.492 14.121 17.723 1 26.5 ? C3D NAD 349 B 1 
HETATM 32 O O3D NAD . . . J 2 10.608 13.665 19.078 1 27.83 ? O3D NAD 349 B 1 
HETATM 33 C C2D NAD . . . J 2 11.692 14.98 17.371 1 27.13 ? C2D NAD 349 B 1 
HETATM 34 O O2D NAD . . . J 2 11.98 15.947 18.385 1 28.5 ? O2D NAD 349 B 1 
HETATM 35 C C1D NAD . . . J 2 12.748 13.885 17.327 1 27.87 ? C1D NAD 349 B 1 
HETATM 36 N N1N NAD . . . J 2 13.975 14.341 16.651 1 30.19 ? N1N NAD 349 B 1 
HETATM 37 C C2N NAD . . . J 2 13.971 14.497 15.258 1 31.04 ? C2N NAD 349 B 1 
HETATM 38 C C3N NAD . . . J 2 15.121 14.921 14.596 1 33.23 ? C3N NAD 349 B 1 
HETATM 39 C C7N NAD . . . J 2 15.057 15.076 13.074 1 34.01 ? C7N NAD 349 B 1 
HETATM 40 O O7N NAD . . . J 2 16.084 15.237 12.404 1 37.46 ? O7N NAD 349 B 1 
HETATM 41 N N7N NAD . . . J 2 13.82 15.035 12.559 1 30.86 ? N7N NAD 349 B 1 
HETATM 42 C C4N NAD . . . J 2 16.291 15.198 15.317 1 34.63 ? C4N NAD 349 B 1 
HETATM 43 C C5N NAD . . . J 2 16.313 15.049 16.708 1 34.62 ? C5N NAD 349 B 1 
HETATM 44 C C6N NAD . . . J 2 15.158 14.619 17.375 1 32.87 ? C6N NAD 349 B 1 
#
_model_server_stats.io_time_ms              23 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           310 
_model_server_stats.encode_time_ms          15 
_model_server_stats.element_count           44 
#