data_3JD1
#
_model_server_result.job_id            4BtYDGJ9lDH6xmEKiAd80Q 
_model_server_result.datetime_utc      '2024-11-01 01:34:40' 
_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          3jd1 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":602}' 
#
_entry.id    3JD1 
#
_exptl.entry_id    3JD1 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              665.441 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE' 
_entity.pdbx_number_of_molecules    12 
_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         90 
_cell.entry_id            3JD1 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               1 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3JD1 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    hexameric 
_pdbx_struct_assembly.oligomeric_count      6 
_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 
_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 G N N 
? 2 H N N 
? 2 I N N 
? 2 J N N 
? 2 K N N 
? 2 L N N 
? 2 M N N 
? 2 N N N 
? 2 O N N 
? 2 P N N 
? 2 Q N N 
? 2 R N N 
#
_chem_comp.formula           'C21 H29 N7 O14 P2' 
_chem_comp.formula_weight    665.441 
_chem_comp.id                NAI 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     NADH 
#
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 NAI doub 235 n n 
PA O2A NAI sing 236 n n 
PA O5B NAI sing 237 n n 
PA O3 NAI sing 238 n n 
O2A HOA2 NAI sing 239 n n 
O5B C5B NAI sing 240 n n 
C5B C4B NAI sing 241 n n 
C5B H51A NAI sing 242 n n 
C5B H52A NAI sing 243 n n 
C4B O4B NAI sing 244 n n 
C4B C3B NAI sing 245 n n 
C4B H4B NAI sing 246 n n 
O4B C1B NAI sing 247 n n 
C3B O3B NAI sing 248 n n 
C3B C2B NAI sing 249 n n 
C3B H3B NAI sing 250 n n 
O3B HO3A NAI sing 251 n n 
C2B O2B NAI sing 252 n n 
C2B C1B NAI sing 253 n n 
C2B H2B NAI sing 254 n n 
O2B HO2A NAI sing 255 n n 
C1B N9A NAI sing 256 n n 
C1B H1B NAI sing 257 n n 
N9A C8A NAI sing 258 n y 
N9A C4A NAI sing 259 n y 
C8A N7A NAI doub 260 n y 
C8A H8A NAI sing 261 n n 
N7A C5A NAI sing 262 n y 
C5A C6A NAI sing 263 n y 
C5A C4A NAI doub 264 n y 
C6A N6A NAI sing 265 n n 
C6A N1A NAI doub 266 n y 
N6A H61A NAI sing 267 n n 
N6A H62A NAI sing 268 n n 
N1A C2A NAI sing 269 n y 
C2A N3A NAI doub 270 n y 
C2A H2A NAI sing 271 n n 
N3A C4A NAI sing 272 n y 
O3 PN NAI sing 273 n n 
PN O1N NAI sing 274 n n 
PN O2N NAI doub 275 n n 
PN O5D NAI sing 276 n n 
O1N HO1N NAI sing 277 n n 
O5D C5D NAI sing 278 n n 
C5D C4D NAI sing 279 n n 
C5D H51N NAI sing 280 n n 
C5D H52N NAI sing 281 n n 
C4D O4D NAI sing 282 n n 
C4D C3D NAI sing 283 n n 
C4D H4D NAI sing 284 n n 
O4D C1D NAI sing 285 n n 
C3D O3D NAI sing 286 n n 
C3D C2D NAI sing 287 n n 
C3D H3D NAI sing 288 n n 
O3D HO3N NAI sing 289 n n 
C2D O2D NAI sing 290 n n 
C2D C1D NAI sing 291 n n 
C2D H2D NAI sing 292 n n 
O2D HO2N NAI sing 293 n n 
C1D N1N NAI sing 294 n n 
C1D H1D NAI sing 295 n n 
N1N C2N NAI sing 296 n n 
N1N C6N NAI sing 297 n n 
C2N C3N NAI doub 298 n n 
C2N H2N NAI sing 299 n n 
C3N C7N NAI sing 300 n n 
C3N C4N NAI sing 301 n n 
C7N O7N NAI doub 302 n n 
C7N N7N NAI sing 303 n n 
N7N H71N NAI sing 304 n n 
N7N H72N NAI sing 305 n n 
C4N C5N NAI sing 306 n n 
C4N H4N NAI sing 307 n n 
C4N H42N NAI sing 308 n n 
C5N C6N NAI doub 309 n n 
C5N H5N NAI sing 310 n n 
C6N H6N NAI sing 311 n n 
#
_atom_sites.entry_id                     3JD1 
_atom_sites.fract_transf_matrix[1][1]    1 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    1 
_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]    1 
_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
G 2 NAI A 1 601 601 NAI NAI . 
H 2 NAI A 1 602 602 NAI NAI . 
I 2 NAI B 1 601 601 NAI NAI . 
J 2 NAI B 1 602 602 NAI NAI . 
K 2 NAI C 1 601 601 NAI NAI . 
L 2 NAI C 1 602 602 NAI NAI . 
M 2 NAI D 1 601 601 NAI NAI . 
N 2 NAI D 1 602 602 NAI NAI . 
O 2 NAI E 1 601 601 NAI NAI . 
P 2 NAI E 1 602 602 NAI NAI . 
Q 2 NAI F 1 601 601 NAI NAI . 
R 2 NAI F 1 602 602 NAI NAI . 
#
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 NAI . . . L 2 82.823 102.681 58.105 1 95.37 ? PA NAI 602 C 1 
HETATM 2 O O1A NAI . . . L 2 81.744 103.494 57.429 1 95.37 ? O1A NAI 602 C 1 
HETATM 3 O O2A NAI . . . L 2 83.13 101.286 57.617 1 95.37 ? O2A NAI 602 C 1 
HETATM 4 O O5B NAI . . . L 2 84.186 103.535 58.083 1 95.37 ? O5B NAI 602 C 1 
HETATM 5 C C5B NAI . . . L 2 84.777 103.989 59.299 1 95.37 ? C5B NAI 602 C 1 
HETATM 6 C C4B NAI . . . L 2 83.971 105.159 59.849 1 95.37 ? C4B NAI 602 C 1 
HETATM 7 O O4B NAI . . . L 2 84.188 105.275 61.258 1 95.37 ? O4B NAI 602 C 1 
HETATM 8 C C3B NAI . . . L 2 84.391 106.47 59.204 1 95.37 ? C3B NAI 602 C 1 
HETATM 9 O O3B NAI . . . L 2 83.275 107.073 58.545 1 95.37 ? O3B NAI 602 C 1 
HETATM 10 C C2B NAI . . . L 2 84.874 107.362 60.33 1 95.37 ? C2B NAI 602 C 1 
HETATM 11 O O2B NAI . . . L 2 84.068 108.542 60.401 1 95.37 ? O2B NAI 602 C 1 
HETATM 12 C C1B NAI . . . L 2 84.726 106.553 61.608 1 95.37 ? C1B NAI 602 C 1 
HETATM 13 N N9A NAI . . . L 2 86.054 106.377 62.247 1 95.37 ? N9A NAI 602 C 1 
HETATM 14 C C8A NAI . . . L 2 87.02 105.534 61.836 1 95.37 ? C8A NAI 602 C 1 
HETATM 15 N N7A NAI . . . L 2 88.114 105.614 62.635 1 95.37 ? N7A NAI 602 C 1 
HETATM 16 C C5A NAI . . . L 2 87.853 106.53 63.586 1 95.37 ? C5A NAI 602 C 1 
HETATM 17 C C6A NAI . . . L 2 88.577 107.1 64.747 1 95.37 ? C6A NAI 602 C 1 
HETATM 18 N N6A NAI . . . L 2 89.832 106.696 65.058 1 95.37 ? N6A NAI 602 C 1 
HETATM 19 N N1A NAI . . . L 2 87.942 108.038 65.484 1 95.37 ? N1A NAI 602 C 1 
HETATM 20 C C2A NAI . . . L 2 86.695 108.449 65.186 1 95.37 ? C2A NAI 602 C 1 
HETATM 21 N N3A NAI . . . L 2 85.981 107.975 64.15 1 95.37 ? N3A NAI 602 C 1 
HETATM 22 C C4A NAI . . . L 2 86.494 107.03 63.325 1 95.37 ? C4A NAI 602 C 1 
HETATM 23 O O3 NAI . . . L 2 82.482 102.602 59.677 1 95.37 ? O3 NAI 602 C 1 
HETATM 24 P PN NAI . . . L 2 83.43 101.769 60.677 1 95.37 ? PN NAI 602 C 1 
HETATM 25 O O1N NAI . . . L 2 84.098 102.745 61.616 1 95.37 ? O1N NAI 602 C 1 
HETATM 26 O O2N NAI . . . L 2 84.267 100.819 59.854 1 95.37 ? O2N NAI 602 C 1 
HETATM 27 O O5D NAI . . . L 2 82.371 100.901 61.525 1 95.37 ? O5D NAI 602 C 1 
HETATM 28 C C5D NAI . . . L 2 82.525 99.489 61.647 1 95.37 ? C5D NAI 602 C 1 
HETATM 29 C C4D NAI . . . L 2 83.904 99.176 62.211 1 95.37 ? C4D NAI 602 C 1 
HETATM 30 O O4D NAI . . . L 2 84.309 100.218 63.102 1 95.37 ? O4D NAI 602 C 1 
HETATM 31 C C3D NAI . . . L 2 83.897 97.871 62.993 1 95.37 ? C3D NAI 602 C 1 
HETATM 32 O O3D NAI . . . L 2 84.819 96.945 62.411 1 95.37 ? O3D NAI 602 C 1 
HETATM 33 C C2D NAI . . . L 2 84.331 98.219 64.403 1 95.37 ? C2D NAI 602 C 1 
HETATM 34 O O2D NAI . . . L 2 85.535 97.521 64.731 1 95.37 ? O2D NAI 602 C 1 
HETATM 35 C C1D NAI . . . L 2 84.579 99.72 64.415 1 95.37 ? C1D NAI 602 C 1 
HETATM 36 N N1N NAI . . . L 2 83.683 100.359 65.38 1 95.37 ? N1N NAI 602 C 1 
HETATM 37 C C2N NAI . . . L 2 84.117 100.594 66.622 1 95.37 ? C2N NAI 602 C 1 
HETATM 38 C C3N NAI . . . L 2 83.309 101.2 67.577 1 95.37 ? C3N NAI 602 C 1 
HETATM 39 C C7N NAI . . . L 2 83.849 101.438 68.955 1 95.37 ? C7N NAI 602 C 1 
HETATM 40 O O7N NAI . . . L 2 84.709 100.695 69.398 1 95.37 ? O7N NAI 602 C 1 
HETATM 41 N N7N NAI . . . L 2 83.375 102.462 69.664 1 95.37 ? N7N NAI 602 C 1 
HETATM 42 C C4N NAI . . . L 2 81.894 101.62 67.252 1 95.37 ? C4N NAI 602 C 1 
HETATM 43 C C5N NAI . . . L 2 81.547 101.308 65.872 1 95.37 ? C5N NAI 602 C 1 
HETATM 44 C C6N NAI . . . L 2 82.446 100.698 65.002 1 95.37 ? C6N NAI 602 C 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    29 
_model_server_stats.query_time_ms           376 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           44 
#