data_2YQ5
#
_model_server_result.job_id            OFj0LbvspQpBpUp60AuesA 
_model_server_result.datetime_utc      '2025-04-03 03:18:05' 
_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          2yq5 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":0}' 
#
_entry.id    2YQ5 
#
_exptl.entry_id    2YQ5 
_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         90 
_cell.entry_id            2YQ5 
_cell.length_a            92.718 
_cell.length_b            110.012 
_cell.length_c            147.736 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2YQ5 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_pdbx_struct_assembly.details               author_and_software_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 
_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 E N N 
? 2 F N N 
? 2 G N N 
? 2 H 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                     2YQ5 
_atom_sites.fract_transf_matrix[1][1]    0.010785 
_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]    0.00909 
_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]    0.006769 
_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 0 0 NAD NAD . 
F 2 NAD B 1 0 0 NAD NAD . 
G 2 NAD C 1 0 0 NAD NAD . 
H 2 NAD D 1 0 0 NAD NAD . 
I 3 HOH A 1 2001 2001 HOH HOH . 
I 3 HOH A 2 2002 2002 HOH HOH . 
I 3 HOH A 3 2003 2003 HOH HOH . 
I 3 HOH A 4 2004 2004 HOH HOH . 
I 3 HOH A 5 2005 2005 HOH HOH . 
I 3 HOH A 6 2006 2006 HOH HOH . 
I 3 HOH A 7 2007 2007 HOH HOH . 
I 3 HOH A 8 2008 2008 HOH HOH . 
I 3 HOH A 9 2009 2009 HOH HOH . 
I 3 HOH A 10 2010 2010 HOH HOH . 
J 3 HOH B 1 2001 2001 HOH HOH . 
J 3 HOH B 2 2002 2002 HOH HOH . 
J 3 HOH B 3 2003 2003 HOH HOH . 
J 3 HOH B 4 2004 2004 HOH HOH . 
J 3 HOH B 5 2005 2005 HOH HOH . 
J 3 HOH B 6 2006 2006 HOH HOH . 
J 3 HOH B 7 2007 2007 HOH HOH . 
J 3 HOH B 8 2008 2008 HOH HOH . 
J 3 HOH B 9 2009 2009 HOH HOH . 
J 3 HOH B 10 2010 2010 HOH HOH . 
J 3 HOH B 11 2011 2011 HOH HOH . 
K 3 HOH C 1 2001 2001 HOH HOH . 
K 3 HOH C 2 2002 2002 HOH HOH . 
K 3 HOH C 3 2003 2003 HOH HOH . 
K 3 HOH C 4 2004 2004 HOH HOH . 
K 3 HOH C 5 2005 2005 HOH HOH . 
K 3 HOH C 6 2006 2006 HOH HOH . 
K 3 HOH C 7 2007 2007 HOH HOH . 
K 3 HOH C 8 2008 2008 HOH HOH . 
K 3 HOH C 9 2009 2009 HOH HOH . 
L 3 HOH D 1 2001 2001 HOH HOH . 
L 3 HOH D 2 2002 2002 HOH HOH . 
L 3 HOH D 3 2003 2003 HOH HOH . 
L 3 HOH D 4 2004 2004 HOH HOH . 
L 3 HOH D 5 2005 2005 HOH HOH . 
L 3 HOH D 6 2006 2006 HOH HOH . 
L 3 HOH D 7 2007 2007 HOH HOH . 
L 3 HOH D 8 2008 2008 HOH HOH . 
L 3 HOH D 9 2009 2009 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 . . . F 2 -20.172 10.615 41.831 1 35.46 ? PA NAD 0 B 1 
HETATM 2 O O1A NAD . . . F 2 -19.49 11.595 41.145 1 33.18 ? O1A NAD 0 B 1 
HETATM 3 O O2A NAD . . . F 2 -21.513 10.63 41.377 1 34.14 ? O2A NAD 0 B 1 
HETATM 4 O O5B NAD . . . F 2 -19.494 9.344 41.643 1 39.18 ? O5B NAD 0 B 1 
HETATM 5 C C5B NAD . . . F 2 -19.917 8.088 42.033 1 36.09 ? C5B NAD 0 B 1 
HETATM 6 C C4B NAD . . . F 2 -19.292 7.025 41.127 1 37.09 ? C4B NAD 0 B 1 
HETATM 7 O O4B NAD . . . F 2 -19.685 5.789 41.562 1 38.4 ? O4B NAD 0 B 1 
HETATM 8 C C3B NAD . . . F 2 -19.864 7.122 39.744 1 36.22 ? C3B NAD 0 B 1 
HETATM 9 O O3B NAD . . . F 2 -18.845 7.071 38.796 1 32.32 ? O3B NAD 0 B 1 
HETATM 10 C C2B NAD . . . F 2 -20.633 5.865 39.582 1 36.25 ? C2B NAD 0 B 1 
HETATM 11 O O2B NAD . . . F 2 -20.476 5.469 38.249 1 31.95 ? O2B NAD 0 B 1 
HETATM 12 C C1B NAD . . . F 2 -19.826 4.976 40.471 1 38.27 ? C1B NAD 0 B 1 
HETATM 13 N N9A NAD . . . F 2 -20.614 3.832 40.936 1 39.23 ? N9A NAD 0 B 1 
HETATM 14 C C8A NAD . . . F 2 -21.902 3.821 41.118 1 38.82 ? C8A NAD 0 B 1 
HETATM 15 N N7A NAD . . . F 2 -22.288 2.651 41.521 1 39.44 ? N7A NAD 0 B 1 
HETATM 16 C C5A NAD . . . F 2 -21.232 1.907 41.608 1 39.1 ? C5A NAD 0 B 1 
HETATM 17 C C6A NAD . . . F 2 -21.028 0.625 41.998 1 40.32 ? C6A NAD 0 B 1 
HETATM 18 N N6A NAD . . . F 2 -22.013 -0.136 42.353 1 40.9 ? N6A NAD 0 B 1 
HETATM 19 N N1A NAD . . . F 2 -19.835 0.129 41.984 1 41.4 ? N1A NAD 0 B 1 
HETATM 20 C C2A NAD . . . F 2 -18.849 0.861 41.6 1 43 ? C2A NAD 0 B 1 
HETATM 21 N N3A NAD . . . F 2 -19.009 2.089 41.25 1 40.61 ? N3A NAD 0 B 1 
HETATM 22 C C4A NAD . . . F 2 -20.182 2.646 41.238 1 38.85 ? C4A NAD 0 B 1 
HETATM 23 O O3 NAD . . . F 2 -19.995 11.108 43.285 1 39.21 ? O3 NAD 0 B 1 
HETATM 24 P PN NAD . . . F 2 -18.856 11.753 43.961 1 39.41 ? PN NAD 0 B 1 
HETATM 25 O O1N NAD . . . F 2 -17.626 11.187 43.598 1 44.79 ? O1N NAD 0 B 1 
HETATM 26 O O2N NAD . . . F 2 -19.017 13.118 44.022 1 41.96 ? O2N NAD 0 B 1 
HETATM 27 O O5D NAD . . . F 2 -19.033 11.325 45.313 1 41.32 ? O5D NAD 0 B 1 
HETATM 28 C C5D NAD . . . F 2 -18.788 9.983 45.717 1 41.72 ? C5D NAD 0 B 1 
HETATM 29 C C4D NAD . . . F 2 -18.976 9.64 47.206 1 41.67 ? C4D NAD 0 B 1 
HETATM 30 O O4D NAD . . . F 2 -18.34 10.496 48.136 1 40.93 ? O4D NAD 0 B 1 
HETATM 31 C C3D NAD . . . F 2 -20.439 9.777 47.474 1 40.78 ? C3D NAD 0 B 1 
HETATM 32 O O3D NAD . . . F 2 -20.853 8.768 48.333 1 45.25 ? O3D NAD 0 B 1 
HETATM 33 C C2D NAD . . . F 2 -20.556 10.972 48.307 1 37.12 ? C2D NAD 0 B 1 
HETATM 34 O O2D NAD . . . F 2 -21.578 10.606 49.149 1 34.86 ? O2D NAD 0 B 1 
HETATM 35 C C1D NAD . . . F 2 -19.284 10.93 49.082 1 38.04 ? C1D NAD 0 B 1 
HETATM 36 N N1N NAD . . . F 2 -18.947 12.262 49.632 1 37.08 ? N1N NAD 0 B 1 
HETATM 37 C C2N NAD . . . F 2 -18.381 12.369 50.852 1 34.54 ? C2N NAD 0 B 1 
HETATM 38 C C3N NAD . . . F 2 -18.073 13.572 51.404 1 35.11 ? C3N NAD 0 B 1 
HETATM 39 C C7N NAD . . . F 2 -17.424 13.619 52.746 1 35.96 ? C7N NAD 0 B 1 
HETATM 40 O O7N NAD . . . F 2 -17.679 14.46 53.575 1 37.93 ? O7N NAD 0 B 1 
HETATM 41 N N7N NAD . . . F 2 -16.591 12.663 52.93 1 31.39 ? N7N NAD 0 B 1 
HETATM 42 C C4N NAD . . . F 2 -18.329 14.707 50.711 1 36.49 ? C4N NAD 0 B 1 
HETATM 43 C C5N NAD . . . F 2 -18.911 14.616 49.486 1 38.83 ? C5N NAD 0 B 1 
HETATM 44 C C6N NAD . . . F 2 -19.204 13.397 48.96 1 38.25 ? C6N NAD 0 B 1 
#
_model_server_stats.io_time_ms              24 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    17 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           44 
#