data_1GPD
#
_model_server_result.job_id            zNw_5wTQykMt7BuReFIpcQ 
_model_server_result.datetime_utc      '2024-12-26 09:49:51' 
_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          1gpd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":339}' 
#
_entry.id    1GPD 
#
_exptl.entry_id    1GPD 
_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    2 
_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            1GPD 
_cell.length_a            149 
_cell.length_b            139.1 
_cell.length_c            80.7 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1GPD 
_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    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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 'point symmetry operation' ? ? -0.170476 -0.748321 -0.640255 -0.74878 -0.324519 0.577934 -0.641323 0.578543 -0.505006 96.24453 70.94252 41.77925 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 H N N 
#
loop_
_struct_conn.conn_type_id
_struct_conn.details
_struct_conn.id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_PDB_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
covale ? covale1 A C ACE 1 G ACE 0 1_555 A N SER 2 G SER 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.319 ? 
covale ? covale2 B C ACE 1 R ACE 0 1_555 B N SER 2 R SER 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? 
#
_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 241 n n 
PA O2A NAD sing 242 n n 
PA O5B NAD sing 243 n n 
PA O3 NAD sing 244 n n 
O2A HOA2 NAD sing 245 n n 
O5B C5B NAD sing 246 n n 
C5B C4B NAD sing 247 n n 
C5B H51A NAD sing 248 n n 
C5B H52A NAD sing 249 n n 
C4B O4B NAD sing 250 n n 
C4B C3B NAD sing 251 n n 
C4B H4B NAD sing 252 n n 
O4B C1B NAD sing 253 n n 
C3B O3B NAD sing 254 n n 
C3B C2B NAD sing 255 n n 
C3B H3B NAD sing 256 n n 
O3B HO3A NAD sing 257 n n 
C2B O2B NAD sing 258 n n 
C2B C1B NAD sing 259 n n 
C2B H2B NAD sing 260 n n 
O2B HO2A NAD sing 261 n n 
C1B N9A NAD sing 262 n n 
C1B H1B NAD sing 263 n n 
N9A C8A NAD sing 264 n y 
N9A C4A NAD sing 265 n y 
C8A N7A NAD doub 266 n y 
C8A H8A NAD sing 267 n n 
N7A C5A NAD sing 268 n y 
C5A C6A NAD sing 269 n y 
C5A C4A NAD doub 270 n y 
C6A N6A NAD sing 271 n n 
C6A N1A NAD doub 272 n y 
N6A H61A NAD sing 273 n n 
N6A H62A NAD sing 274 n n 
N1A C2A NAD sing 275 n y 
C2A N3A NAD doub 276 n y 
C2A H2A NAD sing 277 n n 
N3A C4A NAD sing 278 n y 
O3 PN NAD sing 279 n n 
PN O1N NAD doub 280 n n 
PN O2N NAD sing 281 n n 
PN O5D NAD sing 282 n n 
O5D C5D NAD sing 283 n n 
C5D C4D NAD sing 284 n n 
C5D H51N NAD sing 285 n n 
C5D H52N NAD sing 286 n n 
C4D O4D NAD sing 287 n n 
C4D C3D NAD sing 288 n n 
C4D H4D NAD sing 289 n n 
O4D C1D NAD sing 290 n n 
C3D O3D NAD sing 291 n n 
C3D C2D NAD sing 292 n n 
C3D H3D NAD sing 293 n n 
O3D HO3N NAD sing 294 n n 
C2D O2D NAD sing 295 n n 
C2D C1D NAD sing 296 n n 
C2D H2D NAD sing 297 n n 
O2D HO2N NAD sing 298 n n 
C1D N1N NAD sing 299 n n 
C1D H1D NAD sing 300 n n 
N1N C2N NAD sing 301 n y 
N1N C6N NAD doub 302 n y 
C2N C3N NAD doub 303 n y 
C2N H2N NAD sing 304 n n 
C3N C7N NAD sing 305 n n 
C3N C4N NAD sing 306 n y 
C7N O7N NAD doub 307 n n 
C7N N7N NAD sing 308 n n 
N7N H71N NAD sing 309 n n 
N7N H72N NAD sing 310 n n 
C4N C5N NAD doub 311 n y 
C4N H4N NAD sing 312 n n 
C5N C6N NAD sing 313 n y 
C5N H5N NAD sing 314 n n 
C6N H6N NAD sing 315 n n 
#
_atom_sites.entry_id                     1GPD 
_atom_sites.fract_transf_matrix[1][1]    0.006711 
_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]    0.007189 
_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]    0.012392 
_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 NAD G 1 335 1 NAD NAD . 
D 3 PO4 R 1 335 2 PO4 SPS . 
E 3 PO4 R 1 336 3 PO4 IPS . 
F 3 PO4 R 1 337 2 PO4 SPS . 
G 3 PO4 R 1 338 3 PO4 IPS . 
H 2 NAD R 1 339 1 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 2 47.161 26.455 -4.237 1 0 ? PA NAD 339 R 1 
HETATM 2 O O1A NAD . . . H 2 47.983 27.68 -4.368 1 0 ? O1A NAD 339 R 1 
HETATM 3 O O2A NAD . . . H 2 48.412 26.119 -3.522 1 0 ? O2A NAD 339 R 1 
HETATM 4 O O5B NAD . . . H 2 46.326 26.207 -5.579 1 0 ? O5B NAD 339 R 1 
HETATM 5 C C5B NAD . . . H 2 46.693 26.925 -6.774 1 0 ? C5B NAD 339 R 1 
HETATM 6 C C4B NAD . . . H 2 46.595 26.009 -7.979 1 0 ? C4B NAD 339 R 1 
HETATM 7 O O4B NAD . . . H 2 45.957 26.732 -9.068 1 0 ? O4B NAD 339 R 1 
HETATM 8 C C3B NAD . . . H 2 47.924 25.496 -8.535 1 0 ? C3B NAD 339 R 1 
HETATM 9 O O3B NAD . . . H 2 47.736 24.181 -9.039 1 0 ? O3B NAD 339 R 1 
HETATM 10 C C2B NAD . . . H 2 48.194 26.448 -9.701 1 0 ? C2B NAD 339 R 1 
HETATM 11 O O2B NAD . . . H 2 49.059 25.93 -10.697 1 0 ? O2B NAD 339 R 1 
HETATM 12 C C1B NAD . . . H 2 46.782 26.69 -10.222 1 0 ? C1B NAD 339 R 1 
HETATM 13 N N9A NAD . . . H 2 46.625 27.981 -10.948 1 0 ? N9A NAD 339 R 1 
HETATM 14 C C8A NAD . . . H 2 47.577 28.933 -11.243 1 0 ? C8A NAD 339 R 1 
HETATM 15 N N7A NAD . . . H 2 47.116 29.956 -11.894 1 0 ? N7A NAD 339 R 1 
HETATM 16 C C5A NAD . . . H 2 45.765 29.674 -12.048 1 0 ? C5A NAD 339 R 1 
HETATM 17 C C6A NAD . . . H 2 44.715 30.377 -12.661 1 0 ? C6A NAD 339 R 1 
HETATM 18 N N6A NAD . . . H 2 44.872 31.566 -13.261 1 0 ? N6A NAD 339 R 1 
HETATM 19 N N1A NAD . . . H 2 43.495 29.813 -12.634 1 0 ? N1A NAD 339 R 1 
HETATM 20 C C2A NAD . . . H 2 43.347 28.632 -12.036 1 0 ? C2A NAD 339 R 1 
HETATM 21 N N3A NAD . . . H 2 44.247 27.885 -11.434 1 0 ? N3A NAD 339 R 1 
HETATM 22 C C4A NAD . . . H 2 45.46 28.474 -11.474 1 0 ? C4A NAD 339 R 1 
HETATM 23 O O3 NAD . . . H 2 45.989 26.708 -3.176 1 0 ? O3 NAD 339 R 1 
HETATM 24 P PN NAD . . . H 2 45.883 26.683 -1.58 1 0 ? PN NAD 339 R 1 
HETATM 25 O O1N NAD . . . H 2 44.939 25.771 -0.896 1 0 ? O1N NAD 339 R 1 
HETATM 26 O O2N NAD . . . H 2 47.326 26.485 -1.32 1 0 ? O2N NAD 339 R 1 
HETATM 27 O O5D NAD . . . H 2 45.486 28.201 -1.265 1 0 ? O5D NAD 339 R 1 
HETATM 28 C C5D NAD . . . H 2 45.081 29.055 -2.352 1 0 ? C5D NAD 339 R 1 
HETATM 29 C C4D NAD . . . H 2 43.588 29.308 -2.285 1 0 ? C4D NAD 339 R 1 
HETATM 30 O O4D NAD . . . H 2 43.038 28.411 -1.319 1 0 ? O4D NAD 339 R 1 
HETATM 31 C C3D NAD . . . H 2 43.169 30.707 -1.833 1 0 ? C3D NAD 339 R 1 
HETATM 32 O O3D NAD . . . H 2 41.976 31.071 -2.514 1 0 ? O3D NAD 339 R 1 
HETATM 33 C C2D NAD . . . H 2 42.863 30.506 -0.349 1 0 ? C2D NAD 339 R 1 
HETATM 34 O O2D NAD . . . H 2 41.986 31.47 0.208 1 0 ? O2D NAD 339 R 1 
HETATM 35 C C1D NAD . . . H 2 42.261 29.104 -0.355 1 0 ? C1D NAD 339 R 1 
HETATM 36 N N1N NAD . . . H 2 42.395 28.389 0.946 1 0 ? N1N NAD 339 R 1 
HETATM 37 C C2N NAD . . . H 2 43.594 27.865 1.235 1 0 ? C2N NAD 339 R 1 
HETATM 38 C C3N NAD . . . H 2 43.783 27.188 2.431 1 0 ? C3N NAD 339 R 1 
HETATM 39 C C7N NAD . . . H 2 45.163 26.641 2.653 1 0 ? C7N NAD 339 R 1 
HETATM 40 O O7N NAD . . . H 2 45.414 26.03 3.683 1 0 ? O7N NAD 339 R 1 
HETATM 41 N N7N NAD . . . H 2 46.08 26.855 1.687 1 0 ? N7N NAD 339 R 1 
HETATM 42 C C4N NAD . . . H 2 42.727 27.066 3.304 1 0 ? C4N NAD 339 R 1 
HETATM 43 C C5N NAD . . . H 2 41.513 27.617 2.973 1 0 ? C5N NAD 339 R 1 
HETATM 44 C C6N NAD . . . H 2 41.347 28.281 1.787 1 0 ? C6N NAD 339 R 1 
#
_model_server_stats.io_time_ms              66 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    6 
_model_server_stats.query_time_ms           317 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           44 
#