data_8XD2
#
_model_server_result.job_id            9_ahbv2qQXTwMDSmP7Z_AA 
_model_server_result.datetime_utc      '2024-10-13 19:16:20' 
_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          8xd2 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":501}' 
#
_entry.id    8XD2 
#
_exptl.entry_id    8XD2 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              743.405 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' 
_entity.pdbx_number_of_molecules    1 
_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            8XD2 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8XD2 
_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    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      2 
_struct_asym.id                             B 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_chem_comp.formula           'C21 H28 N7 O17 P3' 
_chem_comp.formula_weight    743.405 
_chem_comp.id                NAP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     "2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE" 
#
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 NAP doub 255 n n 
PA O2A NAP sing 256 n n 
PA O5B NAP sing 257 n n 
PA O3 NAP sing 258 n n 
O2A HOA2 NAP sing 259 n n 
O5B C5B NAP sing 260 n n 
C5B C4B NAP sing 261 n n 
C5B H51A NAP sing 262 n n 
C5B H52A NAP sing 263 n n 
C4B O4B NAP sing 264 n n 
C4B C3B NAP sing 265 n n 
C4B H4B NAP sing 266 n n 
O4B C1B NAP sing 267 n n 
C3B O3B NAP sing 268 n n 
C3B C2B NAP sing 269 n n 
C3B H3B NAP sing 270 n n 
O3B HO3A NAP sing 271 n n 
C2B O2B NAP sing 272 n n 
C2B C1B NAP sing 273 n n 
C2B H2B NAP sing 274 n n 
O2B P2B NAP sing 275 n n 
C1B N9A NAP sing 276 n n 
C1B H1B NAP sing 277 n n 
N9A C8A NAP sing 278 n y 
N9A C4A NAP sing 279 n y 
C8A N7A NAP doub 280 n y 
C8A H8A NAP sing 281 n n 
N7A C5A NAP sing 282 n y 
C5A C6A NAP sing 283 n y 
C5A C4A NAP doub 284 n y 
C6A N6A NAP sing 285 n n 
C6A N1A NAP doub 286 n y 
N6A H61A NAP sing 287 n n 
N6A H62A NAP sing 288 n n 
N1A C2A NAP sing 289 n y 
C2A N3A NAP doub 290 n y 
C2A H2A NAP sing 291 n n 
N3A C4A NAP sing 292 n y 
O3 PN NAP sing 293 n n 
PN O1N NAP doub 294 n n 
PN O2N NAP sing 295 n n 
PN O5D NAP sing 296 n n 
O5D C5D NAP sing 297 n n 
C5D C4D NAP sing 298 n n 
C5D H51N NAP sing 299 n n 
C5D H52N NAP sing 300 n n 
C4D O4D NAP sing 301 n n 
C4D C3D NAP sing 302 n n 
C4D H4D NAP sing 303 n n 
O4D C1D NAP sing 304 n n 
C3D O3D NAP sing 305 n n 
C3D C2D NAP sing 306 n n 
C3D H3D NAP sing 307 n n 
O3D HO3N NAP sing 308 n n 
C2D O2D NAP sing 309 n n 
C2D C1D NAP sing 310 n n 
C2D H2D NAP sing 311 n n 
O2D HO2N NAP sing 312 n n 
C1D N1N NAP sing 313 n n 
C1D H1D NAP sing 314 n n 
N1N C2N NAP sing 315 n y 
N1N C6N NAP doub 316 n y 
C2N C3N NAP doub 317 n y 
C2N H2N NAP sing 318 n n 
C3N C7N NAP sing 319 n n 
C3N C4N NAP sing 320 n y 
C7N O7N NAP doub 321 n n 
C7N N7N NAP sing 322 n n 
N7N H71N NAP sing 323 n n 
N7N H72N NAP sing 324 n n 
C4N C5N NAP doub 325 n y 
C4N H4N NAP sing 326 n n 
C5N C6N NAP sing 327 n y 
C5N H5N NAP sing 328 n n 
C6N H6N NAP sing 329 n n 
P2B O1X NAP doub 330 n n 
P2B O2X NAP sing 331 n n 
P2B O3X NAP sing 332 n n 
O2X HOP2 NAP sing 333 n n 
O3X HOP3 NAP sing 334 n n 
#
_atom_sites.entry_id                     8XD2 
_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
B 2 NAP A 1 501 500 NAP NAP . 
C 3 GGL A 1 502 502 GGL GGL . 
D 4 HOH A 1 601 604 HOH HOH . 
D 4 HOH A 2 602 608 HOH HOH . 
D 4 HOH A 3 603 603 HOH HOH . 
D 4 HOH A 4 604 601 HOH HOH . 
D 4 HOH A 5 605 606 HOH HOH . 
D 4 HOH A 6 606 602 HOH HOH . 
D 4 HOH A 7 607 609 HOH HOH . 
D 4 HOH A 8 608 607 HOH HOH . 
D 4 HOH A 9 609 605 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 NAP . . . B 2 126.332 111.344 119.909 1 16.92 ? PA NAP 501 A 1 
HETATM 2 O O1A NAP . . . B 2 127.087 111.691 118.607 1 22.93 ? O1A NAP 501 A 1 
HETATM 3 O O2A NAP . . . B 2 125.341 112.482 120.256 1 8.93 -1 O2A NAP 501 A 1 
HETATM 4 O O5B NAP . . . B 2 127.413 111.242 121.06 1 21.66 ? O5B NAP 501 A 1 
HETATM 5 C C5B NAP . . . B 2 128.751 111.534 120.765 1 20.36 ? C5B NAP 501 A 1 
HETATM 6 C C4B NAP . . . B 2 129.505 111.765 122.061 1 20.38 ? C4B NAP 501 A 1 
HETATM 7 O O4B NAP . . . B 2 130.705 111.037 122.07 1 25.51 ? O4B NAP 501 A 1 
HETATM 8 C C3B NAP . . . B 2 129.818 113.21 122.221 1 20.79 ? C3B NAP 501 A 1 
HETATM 9 O O3B NAP . . . B 2 130.055 113.517 123.54 1 21.58 ? O3B NAP 501 A 1 
HETATM 10 C C2B NAP . . . B 2 131.062 113.294 121.476 1 21.7 ? C2B NAP 501 A 1 
HETATM 11 O O2B NAP . . . B 2 131.759 114.41 121.889 1 25.73 ? O2B NAP 501 A 1 
HETATM 12 C C1B NAP . . . B 2 131.704 112.024 121.921 1 21.79 ? C1B NAP 501 A 1 
HETATM 13 N N9A NAP . . . B 2 132.747 111.582 121.011 1 24.53 ? N9A NAP 501 A 1 
HETATM 14 C C8A NAP . . . B 2 132.748 111.403 119.559 1 22.4 ? C8A NAP 501 A 1 
HETATM 15 N N7A NAP . . . B 2 134.032 110.957 119.23 1 25.77 ? N7A NAP 501 A 1 
HETATM 16 C C5A NAP . . . B 2 134.772 110.872 120.47 1 22.82 ? C5A NAP 501 A 1 
HETATM 17 C C6A NAP . . . B 2 136.037 110.499 120.687 1 26.52 ? C6A NAP 501 A 1 
HETATM 18 N N6A NAP . . . B 2 136.89 110.095 119.608 1 22.4 ? N6A NAP 501 A 1 
HETATM 19 N N1A NAP . . . B 2 136.462 110.511 121.866 1 22.59 ? N1A NAP 501 A 1 
HETATM 20 C C2A NAP . . . B 2 135.812 110.851 122.951 1 24.14 ? C2A NAP 501 A 1 
HETATM 21 N N3A NAP . . . B 2 134.472 111.266 122.85 1 24.34 ? N3A NAP 501 A 1 
HETATM 22 C C4A NAP . . . B 2 133.992 111.248 121.493 1 24.66 ? C4A NAP 501 A 1 
HETATM 23 O O3 NAP . . . B 2 125.595 109.971 119.732 1 26.54 ? O3 NAP 501 A 1 
HETATM 24 P PN NAP . . . B 2 124.268 109.615 120.51 1 18.71 ? PN NAP 501 A 1 
HETATM 25 O O1N NAP . . . B 2 123.789 110.878 121.265 1 14.97 ? O1N NAP 501 A 1 
HETATM 26 O O2N NAP . . . B 2 124.549 108.468 121.498 1 19.22 -1 O2N NAP 501 A 1 
HETATM 27 O O5D NAP . . . B 2 123.18 109.177 119.483 1 18.24 ? O5D NAP 501 A 1 
HETATM 28 P P2B NAP . . . B 2 131.437 115.837 121.331 1 21.69 ? P2B NAP 501 A 1 
HETATM 29 O O1X NAP . . . B 2 131.856 115.943 119.89 1 27.89 ? O1X NAP 501 A 1 
HETATM 30 O O2X NAP . . . B 2 132.198 116.866 122.12 1 19.59 -1 O2X NAP 501 A 1 
HETATM 31 O O3X NAP . . . B 2 129.959 116.127 121.446 1 20.87 -1 O3X NAP 501 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           279 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           31 
#