data_3JD4
#
_model_server_result.job_id            odSHcS4gJjncqB-EBH37pQ 
_model_server_result.datetime_utc      '2024-11-01 04:43:15' 
_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          3jd4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":601}' 
#
_entry.id    3JD4 
#
_exptl.entry_id    3JD4 
_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            3JD4 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               1 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3JD4 
_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,S,T,U,V,W,X 
_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 I N N 
? 2 J N N 
? 2 L N N 
? 2 M N N 
? 2 N N N 
? 2 P N N 
? 2 R N N 
? 2 S N N 
? 2 U N N 
? 2 V N N 
? 2 W 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 285 n n 
PA O2A NAI sing 286 n n 
PA O5B NAI sing 287 n n 
PA O3 NAI sing 288 n n 
O2A HOA2 NAI sing 289 n n 
O5B C5B NAI sing 290 n n 
C5B C4B NAI sing 291 n n 
C5B H51A NAI sing 292 n n 
C5B H52A NAI sing 293 n n 
C4B O4B NAI sing 294 n n 
C4B C3B NAI sing 295 n n 
C4B H4B NAI sing 296 n n 
O4B C1B NAI sing 297 n n 
C3B O3B NAI sing 298 n n 
C3B C2B NAI sing 299 n n 
C3B H3B NAI sing 300 n n 
O3B HO3A NAI sing 301 n n 
C2B O2B NAI sing 302 n n 
C2B C1B NAI sing 303 n n 
C2B H2B NAI sing 304 n n 
O2B HO2A NAI sing 305 n n 
C1B N9A NAI sing 306 n n 
C1B H1B NAI sing 307 n n 
N9A C8A NAI sing 308 n y 
N9A C4A NAI sing 309 n y 
C8A N7A NAI doub 310 n y 
C8A H8A NAI sing 311 n n 
N7A C5A NAI sing 312 n y 
C5A C6A NAI sing 313 n y 
C5A C4A NAI doub 314 n y 
C6A N6A NAI sing 315 n n 
C6A N1A NAI doub 316 n y 
N6A H61A NAI sing 317 n n 
N6A H62A NAI sing 318 n n 
N1A C2A NAI sing 319 n y 
C2A N3A NAI doub 320 n y 
C2A H2A NAI sing 321 n n 
N3A C4A NAI sing 322 n y 
O3 PN NAI sing 323 n n 
PN O1N NAI sing 324 n n 
PN O2N NAI doub 325 n n 
PN O5D NAI sing 326 n n 
O1N HO1N NAI sing 327 n n 
O5D C5D NAI sing 328 n n 
C5D C4D NAI sing 329 n n 
C5D H51N NAI sing 330 n n 
C5D H52N NAI sing 331 n n 
C4D O4D NAI sing 332 n n 
C4D C3D NAI sing 333 n n 
C4D H4D NAI sing 334 n n 
O4D C1D NAI sing 335 n n 
C3D O3D NAI sing 336 n n 
C3D C2D NAI sing 337 n n 
C3D H3D NAI sing 338 n n 
O3D HO3N NAI sing 339 n n 
C2D O2D NAI sing 340 n n 
C2D C1D NAI sing 341 n n 
C2D H2D NAI sing 342 n n 
O2D HO2N NAI sing 343 n n 
C1D N1N NAI sing 344 n n 
C1D H1D NAI sing 345 n n 
N1N C2N NAI sing 346 n n 
N1N C6N NAI sing 347 n n 
C2N C3N NAI doub 348 n n 
C2N H2N NAI sing 349 n n 
C3N C7N NAI sing 350 n n 
C3N C4N NAI sing 351 n n 
C7N O7N NAI doub 352 n n 
C7N N7N NAI sing 353 n n 
N7N H71N NAI sing 354 n n 
N7N H72N NAI sing 355 n n 
C4N C5N NAI sing 356 n n 
C4N H4N NAI sing 357 n n 
C4N H42N NAI sing 358 n n 
C5N C6N NAI doub 359 n n 
C5N H5N NAI sing 360 n n 
C6N H6N NAI sing 361 n n 
#
_atom_sites.entry_id                     3JD4 
_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 3 GTP A 1 602 602 GTP GTP . 
I 2 NAI A 1 603 603 NAI NAI . 
J 2 NAI B 1 602 601 NAI NAI . 
K 3 GTP B 1 603 602 GTP GTP . 
L 2 NAI B 1 601 603 NAI NAI . 
M 2 NAI C 1 601 603 NAI NAI . 
N 2 NAI C 1 602 601 NAI NAI . 
O 3 GTP C 1 603 602 GTP GTP . 
P 2 NAI D 1 601 601 NAI NAI . 
Q 3 GTP D 1 602 602 GTP GTP . 
R 2 NAI D 1 603 603 NAI NAI . 
S 2 NAI E 1 602 601 NAI NAI . 
T 3 GTP E 1 603 602 GTP GTP . 
U 2 NAI E 1 601 603 NAI NAI . 
V 2 NAI F 1 601 603 NAI NAI . 
W 2 NAI F 1 602 601 NAI NAI . 
X 3 GTP F 1 603 602 GTP GTP . 
#
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 96.915 76.048 53.647 1 82.96 ? PA NAI 601 B 1 
HETATM 2 O O1A NAI . . . L 2 97.3 77.481 53.392 1 51.25 ? O1A NAI 601 B 1 
HETATM 3 O O2A NAI . . . L 2 96.728 75.088 52.502 1 71.06 ? O2A NAI 601 B 1 
HETATM 4 O O5B NAI . . . L 2 97.975 75.415 54.67 1 70.51 ? O5B NAI 601 B 1 
HETATM 5 C C5B NAI . . . L 2 99.182 76.125 54.913 1 66.31 ? C5B NAI 601 B 1 
HETATM 6 C C4B NAI . . . L 2 100.189 75.186 55.543 1 63.84 ? C4B NAI 601 B 1 
HETATM 7 O O4B NAI . . . L 2 99.598 74.509 56.65 1 60.04 ? O4B NAI 601 B 1 
HETATM 8 C C3B NAI . . . L 2 100.607 74.13 54.54 1 63.64 ? C3B NAI 601 B 1 
HETATM 9 O O3B NAI . . . L 2 102.028 74.144 54.388 1 69.8 ? O3B NAI 601 B 1 
HETATM 10 C C2B NAI . . . L 2 100.179 72.815 55.143 1 63.72 ? C2B NAI 601 B 1 
HETATM 11 O O2B NAI . . . L 2 101.211 71.844 54.963 1 67.28 ? O2B NAI 601 B 1 
HETATM 12 C C1B NAI . . . L 2 99.982 73.14 56.609 1 59.9 ? C1B NAI 601 B 1 
HETATM 13 N N9A NAI . . . L 2 98.939 72.264 57.175 1 50.95 ? N9A NAI 601 B 1 
HETATM 14 C C8A NAI . . . L 2 97.721 72.04 56.666 1 53.37 ? C8A NAI 601 B 1 
HETATM 15 N N7A NAI . . . L 2 97.03 71.169 57.44 1 45.05 ? N7A NAI 601 B 1 
HETATM 16 C C5A NAI . . . L 2 97.825 70.82 58.462 1 42.89 ? C5A NAI 601 B 1 
HETATM 17 C C6A NAI . . . L 2 97.728 69.941 59.64 1 45.3 ? C6A NAI 601 B 1 
HETATM 18 N N6A NAI . . . L 2 96.612 69.231 59.899 1 45.98 ? N6A NAI 601 B 1 
HETATM 19 N N1A NAI . . . L 2 98.788 69.862 60.456 1 41.94 ? N1A NAI 601 B 1 
HETATM 20 C C2A NAI . . . L 2 99.905 70.558 60.217 1 41.95 ? C2A NAI 601 B 1 
HETATM 21 N N3A NAI . . . L 2 100.066 71.376 59.171 1 45.12 ? N3A NAI 601 B 1 
HETATM 22 C C4A NAI . . . L 2 99.08 71.54 58.275 1 50.4 ? C4A NAI 601 B 1 
HETATM 23 O O3 NAI . . . L 2 95.582 76.053 54.528 1 70.67 ? O3 NAI 601 B 1 
HETATM 24 P PN NAI . . . L 2 95.456 77.193 55.64 1 65.61 ? PN NAI 601 B 1 
HETATM 25 O O1N NAI . . . L 2 95.071 78.484 54.974 1 62.03 ? O1N NAI 601 B 1 
HETATM 26 O O2N NAI . . . L 2 96.674 77.125 56.517 1 63.77 ? O2N NAI 601 B 1 
HETATM 27 O O5D NAI . . . L 2 94.223 76.672 56.509 1 64.49 ? O5D NAI 601 B 1 
HETATM 28 C C5D NAI . . . L 2 94.487 76.264 57.839 1 57.83 ? C5D NAI 601 B 1 
HETATM 29 C C4D NAI . . . L 2 93.315 76.638 58.718 1 60.91 ? C4D NAI 601 B 1 
HETATM 30 O O4D NAI . . . L 2 93.622 76.246 60.048 1 62.89 ? O4D NAI 601 B 1 
HETATM 31 C C3D NAI . . . L 2 93.126 78.136 58.711 1 50.2 ? C3D NAI 601 B 1 
HETATM 32 O O3D NAI . . . L 2 91.857 78.451 58.144 1 48.82 ? O3D NAI 601 B 1 
HETATM 33 C C2D NAI . . . L 2 93.115 78.551 60.156 1 51.53 ? C2D NAI 601 B 1 
HETATM 34 O O2D NAI . . . L 2 91.819 79.06 60.437 1 52.61 ? O2D NAI 601 B 1 
HETATM 35 C C1D NAI . . . L 2 93.304 77.287 60.962 1 53.76 ? C1D NAI 601 B 1 
HETATM 36 N N1N NAI . . . L 2 94.423 77.444 61.869 1 53.13 ? N1N NAI 601 B 1 
HETATM 37 C C2N NAI . . . L 2 94.295 77.173 63.162 1 57.66 ? C2N NAI 601 B 1 
HETATM 38 C C3N NAI . . . L 2 95.364 77.306 64.031 1 54.92 ? C3N NAI 601 B 1 
HETATM 39 C C7N NAI . . . L 2 95.214 77.015 65.489 1 54.64 ? C7N NAI 601 B 1 
HETATM 40 O O7N NAI . . . L 2 94.1 76.963 65.979 1 53.19 ? O7N NAI 601 B 1 
HETATM 41 N N7N NAI . . . L 2 96.318 76.833 66.209 1 55.75 ? N7N NAI 601 B 1 
HETATM 42 C C4N NAI . . . L 2 96.714 77.756 63.553 1 53.69 ? C4N NAI 601 B 1 
HETATM 43 C C5N NAI . . . L 2 96.708 78.013 62.127 1 53.71 ? C5N NAI 601 B 1 
HETATM 44 C C6N NAI . . . L 2 95.575 77.838 61.353 1 54.16 ? C6N NAI 601 B 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    32 
_model_server_stats.query_time_ms           236 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           44 
#