data_2LDB
#
_model_server_result.job_id            aEr1RPtuGZiZsddYYgVeFg 
_model_server_result.datetime_utc      '2024-10-16 10:23:13' 
_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          2ldb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"N","auth_seq_id":9}' 
#
_entry.id    2LDB 
#
_exptl.entry_id    2LDB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              663.425 
_entity.id                          3 
_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            2LDB 
_cell.length_a            86.8 
_cell.length_b            86.8 
_cell.length_c            356.6 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2LDB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        169 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 61' 
#
_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,J,K,L,M,N,O,P,Q,R,S,T 
_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
? 3 G N N 
? 3 J N N 
? 3 N N N 
? 3 R N 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 K O3 FBP . C FBP 6 1_555 C NE2 GLN 169 C GLN 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? 
covale ? covale2 O O3 FBP . D FBP 2 1_555 D NE2 GLN 169 D GLN 183 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.956 ? 
#
_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 271 n n 
PA O2A NAD sing 272 n n 
PA O5B NAD sing 273 n n 
PA O3 NAD sing 274 n n 
O2A HOA2 NAD sing 275 n n 
O5B C5B NAD sing 276 n n 
C5B C4B NAD sing 277 n n 
C5B H51A NAD sing 278 n n 
C5B H52A NAD sing 279 n n 
C4B O4B NAD sing 280 n n 
C4B C3B NAD sing 281 n n 
C4B H4B NAD sing 282 n n 
O4B C1B NAD sing 283 n n 
C3B O3B NAD sing 284 n n 
C3B C2B NAD sing 285 n n 
C3B H3B NAD sing 286 n n 
O3B HO3A NAD sing 287 n n 
C2B O2B NAD sing 288 n n 
C2B C1B NAD sing 289 n n 
C2B H2B NAD sing 290 n n 
O2B HO2A NAD sing 291 n n 
C1B N9A NAD sing 292 n n 
C1B H1B NAD sing 293 n n 
N9A C8A NAD sing 294 n y 
N9A C4A NAD sing 295 n y 
C8A N7A NAD doub 296 n y 
C8A H8A NAD sing 297 n n 
N7A C5A NAD sing 298 n y 
C5A C6A NAD sing 299 n y 
C5A C4A NAD doub 300 n y 
C6A N6A NAD sing 301 n n 
C6A N1A NAD doub 302 n y 
N6A H61A NAD sing 303 n n 
N6A H62A NAD sing 304 n n 
N1A C2A NAD sing 305 n y 
C2A N3A NAD doub 306 n y 
C2A H2A NAD sing 307 n n 
N3A C4A NAD sing 308 n y 
O3 PN NAD sing 309 n n 
PN O1N NAD doub 310 n n 
PN O2N NAD sing 311 n n 
PN O5D NAD sing 312 n n 
O5D C5D NAD sing 313 n n 
C5D C4D NAD sing 314 n n 
C5D H51N NAD sing 315 n n 
C5D H52N NAD sing 316 n n 
C4D O4D NAD sing 317 n n 
C4D C3D NAD sing 318 n n 
C4D H4D NAD sing 319 n n 
O4D C1D NAD sing 320 n n 
C3D O3D NAD sing 321 n n 
C3D C2D NAD sing 322 n n 
C3D H3D NAD sing 323 n n 
O3D HO3N NAD sing 324 n n 
C2D O2D NAD sing 325 n n 
C2D C1D NAD sing 326 n n 
C2D H2D NAD sing 327 n n 
O2D HO2N NAD sing 328 n n 
C1D N1N NAD sing 329 n n 
C1D H1D NAD sing 330 n n 
N1N C2N NAD sing 331 n y 
N1N C6N NAD doub 332 n y 
C2N C3N NAD doub 333 n y 
C2N H2N NAD sing 334 n n 
C3N C7N NAD sing 335 n n 
C3N C4N NAD sing 336 n y 
C7N O7N NAD doub 337 n n 
C7N N7N NAD sing 338 n n 
N7N H71N NAD sing 339 n n 
N7N H72N NAD sing 340 n n 
C4N C5N NAD doub 341 n y 
C4N H4N NAD sing 342 n n 
C5N C6N NAD sing 343 n y 
C5N H5N NAD sing 344 n n 
C6N H6N NAD sing 345 n n 
#
_atom_sites.entry_id                     2LDB 
_atom_sites.fract_transf_matrix[1][1]    0.011521 
_atom_sites.fract_transf_matrix[1][2]    0.006652 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.013303 
_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]    0.002804 
_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 SO4 A 1 3 3 SO4 SO4 . 
F 2 SO4 A 1 4 4 SO4 SO4 . 
G 3 NAD A 1 1 1 NAD NAD . 
H 2 SO4 B 1 7 3 SO4 SO4 . 
I 2 SO4 B 1 8 4 SO4 SO4 . 
J 3 NAD B 1 5 1 NAD NAD . 
K 4 FBP C 1 6 2 FBP FBP . 
L 2 SO4 C 1 11 3 SO4 SO4 . 
M 2 SO4 C 1 12 4 SO4 SO4 . 
N 3 NAD C 1 9 1 NAD NAD . 
O 4 FBP D 1 2 2 FBP FBP . 
P 2 SO4 D 1 332 3 SO4 SO4 . 
Q 2 SO4 D 1 333 4 SO4 SO4 . 
R 3 NAD D 1 13 1 NAD NAD . 
S 5 HOH A 1 336 336 HOH HOH . 
S 5 HOH A 2 337 337 HOH HOH . 
S 5 HOH A 3 338 338 HOH HOH . 
S 5 HOH A 4 339 339 HOH HOH . 
S 5 HOH A 5 340 340 HOH HOH . 
S 5 HOH A 6 341 341 HOH HOH . 
S 5 HOH A 7 342 342 HOH HOH . 
S 5 HOH A 8 343 343 HOH HOH . 
S 5 HOH A 9 344 344 HOH HOH . 
S 5 HOH A 10 345 345 HOH HOH . 
S 5 HOH A 11 346 346 HOH HOH . 
S 5 HOH A 12 347 347 HOH HOH . 
S 5 HOH A 13 348 348 HOH HOH . 
S 5 HOH A 14 349 349 HOH HOH . 
S 5 HOH A 15 350 350 HOH HOH . 
S 5 HOH A 16 351 351 HOH HOH . 
S 5 HOH A 17 352 352 HOH HOH . 
S 5 HOH A 18 353 353 HOH HOH . 
S 5 HOH A 19 354 354 HOH HOH . 
S 5 HOH A 20 355 355 HOH HOH . 
S 5 HOH A 21 356 356 HOH HOH . 
S 5 HOH A 22 357 357 HOH HOH . 
S 5 HOH A 23 358 358 HOH HOH . 
S 5 HOH A 24 359 359 HOH HOH . 
S 5 HOH A 25 360 360 HOH HOH . 
S 5 HOH A 26 361 361 HOH HOH . 
S 5 HOH A 27 362 362 HOH HOH . 
S 5 HOH A 28 363 363 HOH HOH . 
S 5 HOH A 29 364 364 HOH HOH . 
S 5 HOH A 30 365 365 HOH HOH . 
S 5 HOH A 31 366 366 HOH HOH . 
S 5 HOH A 32 367 367 HOH HOH . 
S 5 HOH A 33 368 368 HOH HOH . 
S 5 HOH A 34 369 369 HOH HOH . 
S 5 HOH A 35 370 370 HOH HOH . 
S 5 HOH A 36 371 371 HOH HOH . 
S 5 HOH A 37 372 372 HOH HOH . 
S 5 HOH A 38 375 375 HOH HOH . 
S 5 HOH A 39 376 376 HOH HOH . 
S 5 HOH A 40 377 377 HOH HOH . 
S 5 HOH A 41 378 378 HOH HOH . 
S 5 HOH A 42 379 379 HOH HOH . 
S 5 HOH A 43 380 380 HOH HOH . 
S 5 HOH A 44 381 381 HOH HOH . 
S 5 HOH A 45 382 382 HOH HOH . 
S 5 HOH A 46 383 383 HOH HOH . 
S 5 HOH A 47 384 384 HOH HOH . 
T 5 HOH C 1 373 373 HOH HOH . 
T 5 HOH C 2 374 374 HOH HOH . 
T 5 HOH C 3 385 385 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 . . . N 3 12.851 36.743 207.426 1 22.08 ? PA NAD 9 C 1 
HETATM 2 O O1A NAD . . . N 3 13.292 36.964 208.866 1 22.33 ? O1A NAD 9 C 1 
HETATM 3 O O2A NAD . . . N 3 12.734 38.06 206.757 1 21.88 ? O2A NAD 9 C 1 
HETATM 4 O O5B NAD . . . N 3 11.431 35.963 207.537 1 20.61 ? O5B NAD 9 C 1 
HETATM 5 C C5B NAD . . . N 3 10.75 35.642 206.292 1 19.1 ? C5B NAD 9 C 1 
HETATM 6 C C4B NAD . . . N 3 9.296 35.648 206.459 1 18.27 ? C4B NAD 9 C 1 
HETATM 7 O O4B NAD . . . N 3 8.778 34.309 206.761 1 17.65 ? O4B NAD 9 C 1 
HETATM 8 C C3B NAD . . . N 3 8.575 36.611 207.405 1 18.16 ? C3B NAD 9 C 1 
HETATM 9 O O3B NAD . . . N 3 7.946 37.673 206.643 1 18.08 ? O3B NAD 9 C 1 
HETATM 10 C C2B NAD . . . N 3 7.535 35.724 208.081 1 17.99 ? C2B NAD 9 C 1 
HETATM 11 O O2B NAD . . . N 3 6.288 36.306 208.441 1 18 ? O2B NAD 9 C 1 
HETATM 12 C C1B NAD . . . N 3 7.37 34.577 207.011 1 17.44 ? C1B NAD 9 C 1 
HETATM 13 N N9A NAD . . . N 3 6.913 33.344 207.654 1 17.01 ? N9A NAD 9 C 1 
HETATM 14 C C8A NAD . . . N 3 7.494 32.745 208.729 1 16.77 ? C8A NAD 9 C 1 
HETATM 15 N N7A NAD . . . N 3 6.783 31.69 209.152 1 16.94 ? N7A NAD 9 C 1 
HETATM 16 C C5A NAD . . . N 3 5.718 31.606 208.29 1 16.39 ? C5A NAD 9 C 1 
HETATM 17 C C6A NAD . . . N 3 4.702 30.641 208.153 1 16.09 ? C6A NAD 9 C 1 
HETATM 18 N N6A NAD . . . N 3 4.566 29.626 209.004 1 15.87 ? N6A NAD 9 C 1 
HETATM 19 N N1A NAD . . . N 3 3.837 30.796 207.116 1 16.14 ? N1A NAD 9 C 1 
HETATM 20 C C2A NAD . . . N 3 3.974 31.911 206.289 1 16.02 ? C2A NAD 9 C 1 
HETATM 21 N N3A NAD . . . N 3 4.885 32.843 206.341 1 16.41 ? N3A NAD 9 C 1 
HETATM 22 C C4A NAD . . . N 3 5.772 32.621 207.348 1 16.77 ? C4A NAD 9 C 1 
HETATM 23 O O3 NAD . . . N 3 13.749 35.683 206.685 1 21.76 ? O3 NAD 9 C 1 
HETATM 24 P PN NAD . . . N 3 14.744 35.744 205.478 1 22.78 ? PN NAD 9 C 1 
HETATM 25 O O1N NAD . . . N 3 16.08 36.347 205.857 1 22.37 ? O1N NAD 9 C 1 
HETATM 26 O O2N NAD . . . N 3 14.136 36.576 204.402 1 22.32 ? O2N NAD 9 C 1 
HETATM 27 O O5D NAD . . . N 3 14.932 34.188 205.075 1 22.9 ? O5D NAD 9 C 1 
HETATM 28 C C5D NAD . . . N 3 14.141 33.095 205.633 1 22.43 ? C5D NAD 9 C 1 
HETATM 29 C C4D NAD . . . N 3 14.959 31.845 205.321 1 22.49 ? C4D NAD 9 C 1 
HETATM 30 O O4D NAD . . . N 3 15.752 32.3 204.105 1 22.5 ? O4D NAD 9 C 1 
HETATM 31 C C3D NAD . . . N 3 16.02 31.523 206.398 1 22.73 ? C3D NAD 9 C 1 
HETATM 32 O O3D NAD . . . N 3 16.053 30.125 206.71 1 22.6 ? O3D NAD 9 C 1 
HETATM 33 C C2D NAD . . . N 3 17.336 31.933 205.745 1 23.01 ? C2D NAD 9 C 1 
HETATM 34 O O2D NAD . . . N 3 18.531 31.276 206.111 1 22.47 ? O2D NAD 9 C 1 
HETATM 35 C C1D NAD . . . N 3 16.987 31.611 204.28 1 23.19 ? C1D NAD 9 C 1 
HETATM 36 N N1N NAD . . . N 3 18.08 31.954 203.392 1 23.53 ? N1N NAD 9 C 1 
HETATM 37 C C2N NAD . . . N 3 18.629 30.933 202.672 1 23.82 ? C2N NAD 9 C 1 
HETATM 38 C C3N NAD . . . N 3 19.68 31.168 201.85 1 24.14 ? C3N NAD 9 C 1 
HETATM 39 C C7N NAD . . . N 3 20.357 30.134 200.907 1 24.86 ? C7N NAD 9 C 1 
HETATM 40 O O7N NAD . . . N 3 21.373 30.5 200.283 1 25.92 ? O7N NAD 9 C 1 
HETATM 41 N N7N NAD . . . N 3 19.766 28.956 200.717 1 25.02 ? N7N NAD 9 C 1 
HETATM 42 C C4N NAD . . . N 3 20.205 32.463 201.656 1 23.81 ? C4N NAD 9 C 1 
HETATM 43 C C5N NAD . . . N 3 19.643 33.409 202.493 1 23.55 ? C5N NAD 9 C 1 
HETATM 44 C C6N NAD . . . N 3 18.664 33.242 203.427 1 23.55 ? C6N NAD 9 C 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    28 
_model_server_stats.query_time_ms           272 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           44 
#