data_3GPD
#
_model_server_result.job_id            2fMTkOyJqrP3twaI6OO7WQ 
_model_server_result.datetime_utc      '2025-03-04 21:38:30' 
_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          3gpd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":336}' 
#
_entry.id    3GPD 
#
_exptl.entry_id    3GPD 
_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    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          114.3 
_cell.angle_gamma         90 
_cell.entry_id            3GPD 
_cell.length_a            132.4 
_cell.length_b            97.9 
_cell.length_c            81.6 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3GPD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
_pdbx_struct_assembly.method_details        PISA,PQS 
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 E N N 
? 3 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 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                     3GPD 
_atom_sites.fract_transf_matrix[1][1]    0.007553 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.00341 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.010215 
_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]    0.013446 
_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
C 2 SO4 R 1 338 338 SO4 IPS . 
D 2 SO4 R 1 340 340 SO4 SPS . 
E 3 NAD R 1 336 336 NAD NAD . 
F 2 SO4 G 1 338 338 SO4 IPS . 
G 2 SO4 G 1 340 340 SO4 SPS . 
H 3 NAD G 1 336 336 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 . . . H 3 -3.984 9.475 18.225 1 0 ? PA NAD 336 G 1 
HETATM 2 O O1A NAD . . . H 3 -3.866 8.017 18.457 1 0 ? O1A NAD 336 G 1 
HETATM 3 O O2A NAD . . . H 3 -3.257 9.819 16.983 1 0 ? O2A NAD 336 G 1 
HETATM 4 O O5B NAD . . . H 3 -3.344 10.26 19.445 1 0 ? O5B NAD 336 G 1 
HETATM 5 C C5B NAD . . . H 3 -4.029 10.235 20.668 1 0 ? C5B NAD 336 G 1 
HETATM 6 C C4B NAD . . . H 3 -3.033 10.319 21.81 1 0 ? C4B NAD 336 G 1 
HETATM 7 O O4B NAD . . . H 3 -3.574 11.158 22.873 1 0 ? O4B NAD 336 G 1 
HETATM 8 C C3B NAD . . . H 3 -2.845 9.063 22.301 1 0 ? C3B NAD 336 G 1 
HETATM 9 O O3B NAD . . . H 3 -1.461 8.629 22.184 1 0 ? O3B NAD 336 G 1 
HETATM 10 C C2B NAD . . . H 3 -3.216 9.33 23.538 1 0 ? C2B NAD 336 G 1 
HETATM 11 O O2B NAD . . . H 3 -3.844 8.38 24.139 1 0 ? O2B NAD 336 G 1 
HETATM 12 C C1B NAD . . . H 3 -3.256 10.656 24.132 1 0 ? C1B NAD 336 G 1 
HETATM 13 N N9A NAD . . . H 3 -4.389 10.682 25.191 1 0 ? N9A NAD 336 G 1 
HETATM 14 C C8A NAD . . . H 3 -5.606 11.371 25.282 1 0 ? C8A NAD 336 G 1 
HETATM 15 N N7A NAD . . . H 3 -5.589 11.827 26.668 1 0 ? N7A NAD 336 G 1 
HETATM 16 C C5A NAD . . . H 3 -4.452 11.117 27.419 1 0 ? C5A NAD 336 G 1 
HETATM 17 C C6A NAD . . . H 3 -3.951 10.972 28.819 1 0 ? C6A NAD 336 G 1 
HETATM 18 N N6A NAD . . . H 3 -4.267 11.829 29.788 1 0 ? N6A NAD 336 G 1 
HETATM 19 N N1A NAD . . . H 3 -3.112 9.898 29.122 1 0 ? N1A NAD 336 G 1 
HETATM 20 C C2A NAD . . . H 3 -2.737 9.065 28.102 1 0 ? C2A NAD 336 G 1 
HETATM 21 N N3A NAD . . . H 3 -3.041 9.147 26.813 1 0 ? N3A NAD 336 G 1 
HETATM 22 C C4A NAD . . . H 3 -3.937 10.18 26.521 1 0 ? C4A NAD 336 G 1 
HETATM 23 O O3 NAD . . . H 3 -5.476 10.042 18.34 1 0 ? O3 NAD 336 G 1 
HETATM 24 P PN NAD . . . H 3 -6.806 10.253 17.339 1 0 ? PN NAD 336 G 1 
HETATM 25 O O1N NAD . . . H 3 -6.77 9.287 16.219 1 0 ? O1N NAD 336 G 1 
HETATM 26 O O2N NAD . . . H 3 -6.801 11.625 16.778 1 0 ? O2N NAD 336 G 1 
HETATM 27 O O5D NAD . . . H 3 -8.038 9.945 18.358 1 0 ? O5D NAD 336 G 1 
HETATM 28 C C5D NAD . . . H 3 -8.923 11.025 18.768 1 0 ? C5D NAD 336 G 1 
HETATM 29 C C4D NAD . . . H 3 -10.419 10.626 18.726 1 0 ? C4D NAD 336 G 1 
HETATM 30 O O4D NAD . . . H 3 -11.111 11.265 17.566 1 0 ? O4D NAD 336 G 1 
HETATM 31 C C3D NAD . . . H 3 -10.742 9.156 18.585 1 0 ? C3D NAD 336 G 1 
HETATM 32 O O3D NAD . . . H 3 -10.773 8.424 19.827 1 0 ? O3D NAD 336 G 1 
HETATM 33 C C2D NAD . . . H 3 -12.164 9.227 17.939 1 0 ? C2D NAD 336 G 1 
HETATM 34 O O2D NAD . . . H 3 -13.123 9.404 19 1 0 ? O2D NAD 336 G 1 
HETATM 35 C C1D NAD . . . H 3 -12.171 10.461 16.998 1 0 ? C1D NAD 336 G 1 
HETATM 36 N N1N NAD . . . H 3 -12.075 10.407 15.367 1 0 ? N1N NAD 336 G 1 
HETATM 37 C C2N NAD . . . H 3 -11.037 9.793 14.564 1 0 ? C2N NAD 336 G 1 
HETATM 38 C C3N NAD . . . H 3 -10.989 9.927 13.202 1 0 ? C3N NAD 336 G 1 
HETATM 39 C C7N NAD . . . H 3 -9.563 9.397 12.683 1 0 ? C7N NAD 336 G 1 
HETATM 40 O O7N NAD . . . H 3 -9.441 8.949 11.556 1 0 ? O7N NAD 336 G 1 
HETATM 41 N N7N NAD . . . H 3 -8.543 9.492 13.568 1 0 ? N7N NAD 336 G 1 
HETATM 42 C C4N NAD . . . H 3 -11.975 10.618 12.464 1 0 ? C4N NAD 336 G 1 
HETATM 43 C C5N NAD . . . H 3 -12.979 11.139 13.276 1 0 ? C5N NAD 336 G 1 
HETATM 44 C C6N NAD . . . H 3 -13.106 11.087 14.644 1 0 ? C6N NAD 336 G 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           5 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           250 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           44 
#