data_8ZC9
#
_model_server_result.job_id            P5YTJWaVkmQeXKX0SZnOEw 
_model_server_result.datetime_utc      '2024-11-22 10:26:45' 
_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          8zc9 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"G","auth_seq_id":1101}' 
#
_entry.id    8ZC9 
#
_exptl.entry_id    8ZC9 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_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         90 
_cell.entry_id            8ZC9 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8ZC9 
_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 
_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    ? 
_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 H N N 
? 3 I N N 
? 3 J 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 235 n n 
PA O2A NAD sing 236 n n 
PA O5B NAD sing 237 n n 
PA O3 NAD sing 238 n n 
O2A HOA2 NAD sing 239 n n 
O5B C5B NAD sing 240 n n 
C5B C4B NAD sing 241 n n 
C5B H51A NAD sing 242 n n 
C5B H52A NAD sing 243 n n 
C4B O4B NAD sing 244 n n 
C4B C3B NAD sing 245 n n 
C4B H4B NAD sing 246 n n 
O4B C1B NAD sing 247 n n 
C3B O3B NAD sing 248 n n 
C3B C2B NAD sing 249 n n 
C3B H3B NAD sing 250 n n 
O3B HO3A NAD sing 251 n n 
C2B O2B NAD sing 252 n n 
C2B C1B NAD sing 253 n n 
C2B H2B NAD sing 254 n n 
O2B HO2A NAD sing 255 n n 
C1B N9A NAD sing 256 n n 
C1B H1B NAD sing 257 n n 
N9A C8A NAD sing 258 n y 
N9A C4A NAD sing 259 n y 
C8A N7A NAD doub 260 n y 
C8A H8A NAD sing 261 n n 
N7A C5A NAD sing 262 n y 
C5A C6A NAD sing 263 n y 
C5A C4A NAD doub 264 n y 
C6A N6A NAD sing 265 n n 
C6A N1A NAD doub 266 n y 
N6A H61A NAD sing 267 n n 
N6A H62A NAD sing 268 n n 
N1A C2A NAD sing 269 n y 
C2A N3A NAD doub 270 n y 
C2A H2A NAD sing 271 n n 
N3A C4A NAD sing 272 n y 
O3 PN NAD sing 273 n n 
PN O1N NAD doub 274 n n 
PN O2N NAD sing 275 n n 
PN O5D NAD sing 276 n n 
O5D C5D NAD sing 277 n n 
C5D C4D NAD sing 278 n n 
C5D H51N NAD sing 279 n n 
C5D H52N NAD sing 280 n n 
C4D O4D NAD sing 281 n n 
C4D C3D NAD sing 282 n n 
C4D H4D NAD sing 283 n n 
O4D C1D NAD sing 284 n n 
C3D O3D NAD sing 285 n n 
C3D C2D NAD sing 286 n n 
C3D H3D NAD sing 287 n n 
O3D HO3N NAD sing 288 n n 
C2D O2D NAD sing 289 n n 
C2D C1D NAD sing 290 n n 
C2D H2D NAD sing 291 n n 
O2D HO2N NAD sing 292 n n 
C1D N1N NAD sing 293 n n 
C1D H1D NAD sing 294 n n 
N1N C2N NAD sing 295 n y 
N1N C6N NAD doub 296 n y 
C2N C3N NAD doub 297 n y 
C2N H2N NAD sing 298 n n 
C3N C7N NAD sing 299 n n 
C3N C4N NAD sing 300 n y 
C7N O7N NAD doub 301 n n 
C7N N7N NAD sing 302 n n 
N7N H71N NAD sing 303 n n 
N7N H72N NAD sing 304 n n 
C4N C5N NAD doub 305 n y 
C4N H4N NAD sing 306 n n 
C5N C6N NAD sing 307 n y 
C5N H5N NAD sing 308 n n 
C6N H6N NAD sing 309 n n 
#
_atom_sites.entry_id                     8ZC9 
_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 3 NAD B 1 1101 1101 NAD NAD . 
H 3 NAD A 1 1101 1101 NAD NAD . 
I 3 NAD E 1 1101 1101 NAD NAD . 
J 3 NAD D 1 1101 1101 NAD NAD . 
#
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 . . . G 3 210.363 244.228 218.75 1 105.91 ? PA NAD 1101 B 1 
HETATM 2 O O1A NAD . . . G 3 209.782 245.585 219.093 1 107.37 ? O1A NAD 1101 B 1 
HETATM 3 O O2A NAD . . . G 3 209.24 243.325 218.279 1 101.12 ? O2A NAD 1101 B 1 
HETATM 4 O O5B NAD . . . G 3 211.135 243.644 220.047 1 107.03 ? O5B NAD 1101 B 1 
HETATM 5 C C5B NAD . . . G 3 210.865 242.396 220.595 1 102.26 ? C5B NAD 1101 B 1 
HETATM 6 C C4B NAD . . . G 3 210.295 242.569 222.055 1 98.57 ? C4B NAD 1101 B 1 
HETATM 7 O O4B NAD . . . G 3 211.198 243.53 222.9 1 100.25 ? O4B NAD 1101 B 1 
HETATM 8 C C3B NAD . . . G 3 209.156 243.147 222.052 1 96.95 ? C3B NAD 1101 B 1 
HETATM 9 O O3B NAD . . . G 3 208.081 242.151 222.136 1 105.6 ? O3B NAD 1101 B 1 
HETATM 10 C C2B NAD . . . G 3 209.113 244.128 223.414 1 96.47 ? C2B NAD 1101 B 1 
HETATM 11 O O2B NAD . . . G 3 207.963 243.775 224.223 1 103.85 ? O2B NAD 1101 B 1 
HETATM 12 C C1B NAD . . . G 3 210.197 243.871 224.049 1 102.8 ? C1B NAD 1101 B 1 
HETATM 13 N N9A NAD . . . G 3 210.704 244.976 224.937 1 106.87 ? N9A NAD 1101 B 1 
HETATM 14 C C8A NAD . . . G 3 210.839 245.199 226.253 1 104.1 ? C8A NAD 1101 B 1 
HETATM 15 N N7A NAD . . . G 3 211.395 246.423 226.432 1 92.83 ? N7A NAD 1101 B 1 
HETATM 16 C C5A NAD . . . G 3 211.611 246.955 225.21 1 91.56 ? C5A NAD 1101 B 1 
HETATM 17 C C6A NAD . . . G 3 212.146 248.155 224.829 1 98.87 ? C6A NAD 1101 B 1 
HETATM 18 N N6A NAD . . . G 3 212.664 249.271 225.587 1 101.8 ? N6A NAD 1101 B 1 
HETATM 19 N N1A NAD . . . G 3 212.254 248.453 223.549 1 106.62 ? N1A NAD 1101 B 1 
HETATM 20 C C2A NAD . . . G 3 211.832 247.562 222.606 1 106.37 ? C2A NAD 1101 B 1 
HETATM 21 N N3A NAD . . . G 3 211.308 246.383 222.977 1 98.28 ? N3A NAD 1101 B 1 
HETATM 22 C C4A NAD . . . G 3 211.199 246.076 224.283 1 96.16 ? C4A NAD 1101 B 1 
HETATM 23 O O3 NAD . . . G 3 211.463 244.415 217.56 1 102.21 ? O3 NAD 1101 B 1 
HETATM 24 P PN NAD . . . G 3 213.079 244.814 217.816 1 120.75 ? PN NAD 1101 B 1 
HETATM 25 O O1N NAD . . . G 3 213.933 244.295 216.62 1 106.31 ? O1N NAD 1101 B 1 
HETATM 26 O O2N NAD . . . G 3 213.596 244.154 219.138 1 112.41 ? O2N NAD 1101 B 1 
HETATM 27 O O5D NAD . . . G 3 213.245 246.444 217.921 1 111.77 ? O5D NAD 1101 B 1 
HETATM 28 C C5D NAD . . . G 3 212.864 247.158 219.173 1 103.45 ? C5D NAD 1101 B 1 
HETATM 29 C C4D NAD . . . G 3 213.275 248.628 219.042 1 106.27 ? C4D NAD 1101 B 1 
HETATM 30 O O4D NAD . . . G 3 214.596 248.697 218.243 1 111.24 ? O4D NAD 1101 B 1 
HETATM 31 C C3D NAD . . . G 3 212.421 249.318 218.371 1 107.07 ? C3D NAD 1101 B 1 
HETATM 32 O O3D NAD . . . G 3 211.564 250.073 219.299 1 105.38 ? O3D NAD 1101 B 1 
HETATM 33 C C2D NAD . . . G 3 213.277 250.37 217.451 1 108.2 ? C2D NAD 1101 B 1 
HETATM 34 O O2D NAD . . . G 3 213.449 251.656 218.211 1 106.19 ? O2D NAD 1101 B 1 
HETATM 35 C C1D NAD . . . G 3 214.442 249.856 217.237 1 107.92 ? C1D NAD 1101 B 1 
HETATM 36 N N1N NAD . . . G 3 214.623 249.317 215.821 1 105.81 ? N1N NAD 1101 B 1 
HETATM 37 C C2N NAD . . . G 3 213.835 248.328 215.331 1 104.01 ? C2N NAD 1101 B 1 
HETATM 38 C C3N NAD . . . G 3 214.024 247.837 214.014 1 109.44 ? C3N NAD 1101 B 1 
HETATM 39 C C7N NAD . . . G 3 213.115 246.705 213.442 1 110.04 ? C7N NAD 1101 B 1 
HETATM 40 O O7N NAD . . . G 3 213.489 246.065 212.481 1 110.41 ? O7N NAD 1101 B 1 
HETATM 41 N N7N NAD . . . G 3 211.873 246.412 214.006 1 103.93 ? N7N NAD 1101 B 1 
HETATM 42 C C4N NAD . . . G 3 215.006 248.35 213.246 1 107.49 ? C4N NAD 1101 B 1 
HETATM 43 C C5N NAD . . . G 3 215.814 249.346 213.734 1 104.56 ? C5N NAD 1101 B 1 
HETATM 44 C C6N NAD . . . G 3 215.615 249.826 215.038 1 104.61 ? C6N NAD 1101 B 1 
HETATM 45 H H51A NAD . . . G 3 211.794 241.834 220.652 1 101.75 ? H51A NAD 1101 B 1 
HETATM 46 H H52A NAD . . . G 3 210.119 241.813 219.961 1 102.23 ? H52A NAD 1101 B 1 
HETATM 47 H H4B NAD . . . G 3 210.217 241.579 222.563 1 100.91 ? H4B NAD 1101 B 1 
HETATM 48 H H3B NAD . . . G 3 209.048 243.74 221.169 1 102.15 ? H3B NAD 1101 B 1 
HETATM 49 H HO3A NAD . . . G 3 207.699 242.177 222.982 1 101.27 ? HO3A NAD 1101 B 1 
HETATM 50 H H2B NAD . . . G 3 209.046 245.245 223.085 1 100.24 ? H2B NAD 1101 B 1 
HETATM 51 H HO2A NAD . . . G 3 208.197 243.875 225.209 1 101.18 ? HO2A NAD 1101 B 1 
HETATM 52 H H1B NAD . . . G 3 210.043 242.968 224.658 1 101.38 ? H1B NAD 1101 B 1 
HETATM 53 H H8A NAD . . . G 3 210.536 244.485 227.077 1 99.97 ? H8A NAD 1101 B 1 
HETATM 54 H H61A NAD . . . G 3 212.863 250.15 225.123 1 103.04 ? H61A NAD 1101 B 1 
HETATM 55 H H62A NAD . . . G 3 212.822 249.179 226.542 1 100.92 ? H62A NAD 1101 B 1 
HETATM 56 H H2A NAD . . . G 3 211.922 247.808 221.55 1 103.12 ? H2A NAD 1101 B 1 
HETATM 57 H H51N NAD . . . G 3 213.43 246.687 220.066 1 102.42 ? H51N NAD 1101 B 1 
HETATM 58 H H52N NAD . . . G 3 211.784 247.074 219.35 1 102.54 ? H52N NAD 1101 B 1 
HETATM 59 H H4D NAD . . . G 3 213.41 249.052 219.985 1 102.85 ? H4D NAD 1101 B 1 
HETATM 60 H H3D NAD . . . G 3 211.762 248.637 217.694 1 103.02 ? H3D NAD 1101 B 1 
HETATM 61 H HO3N NAD . . . G 3 211.201 249.473 219.958 1 102.52 ? HO3N NAD 1101 B 1 
HETATM 62 H H2D NAD . . . G 3 212.727 250.574 216.466 1 102.66 ? H2D NAD 1101 B 1 
HETATM 63 H HO2N NAD . . . G 3 213.863 251.491 218.998 1 102.84 ? HO2N NAD 1101 B 1 
HETATM 64 H H1D NAD . . . G 3 215.228 250.633 217.446 1 102.26 ? H1D NAD 1101 B 1 
HETATM 65 H H2N NAD . . . G 3 213.037 247.911 215.954 1 102.69 ? H2N NAD 1101 B 1 
HETATM 66 H H71N NAD . . . G 3 211.298 245.666 213.607 1 102.51 ? H71N NAD 1101 B 1 
HETATM 67 H H72N NAD . . . G 3 211.514 246.958 214.846 1 102.61 ? H72N NAD 1101 B 1 
HETATM 68 H H4N NAD . . . G 3 215.157 247.968 212.219 1 103.28 ? H4N NAD 1101 B 1 
HETATM 69 H H5N NAD . . . G 3 216.585 249.751 213.129 1 102.39 ? H5N NAD 1101 B 1 
HETATM 70 H H6N NAD . . . G 3 216.461 250.537 214.898 1 102.27 ? H6N NAD 1101 B 1 
#
_model_server_stats.io_time_ms              43 
_model_server_stats.parse_time_ms           15 
_model_server_stats.create_model_time_ms    37 
_model_server_stats.query_time_ms           273 
_model_server_stats.encode_time_ms          9 
_model_server_stats.element_count           70 
#