data_2YDB
#
_model_server_result.job_id            UohgTdI1QGFrZsRPhbhmww 
_model_server_result.datetime_utc      '2024-12-02 21:08:32' 
_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          2ydb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":1379}' 
#
_entry.id    2YDB 
#
_exptl.entry_id    2YDB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_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            2YDB 
_cell.length_a            41.74 
_cell.length_b            46.81 
_cell.length_c            106.88 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2YDB 
_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    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 
_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 237 n n 
PA O2A NAP sing 238 n n 
PA O5B NAP sing 239 n n 
PA O3 NAP sing 240 n n 
O2A HOA2 NAP sing 241 n n 
O5B C5B NAP sing 242 n n 
C5B C4B NAP sing 243 n n 
C5B H51A NAP sing 244 n n 
C5B H52A NAP sing 245 n n 
C4B O4B NAP sing 246 n n 
C4B C3B NAP sing 247 n n 
C4B H4B NAP sing 248 n n 
O4B C1B NAP sing 249 n n 
C3B O3B NAP sing 250 n n 
C3B C2B NAP sing 251 n n 
C3B H3B NAP sing 252 n n 
O3B HO3A NAP sing 253 n n 
C2B O2B NAP sing 254 n n 
C2B C1B NAP sing 255 n n 
C2B H2B NAP sing 256 n n 
O2B P2B NAP sing 257 n n 
C1B N9A NAP sing 258 n n 
C1B H1B NAP sing 259 n n 
N9A C8A NAP sing 260 n y 
N9A C4A NAP sing 261 n y 
C8A N7A NAP doub 262 n y 
C8A H8A NAP sing 263 n n 
N7A C5A NAP sing 264 n y 
C5A C6A NAP sing 265 n y 
C5A C4A NAP doub 266 n y 
C6A N6A NAP sing 267 n n 
C6A N1A NAP doub 268 n y 
N6A H61A NAP sing 269 n n 
N6A H62A NAP sing 270 n n 
N1A C2A NAP sing 271 n y 
C2A N3A NAP doub 272 n y 
C2A H2A NAP sing 273 n n 
N3A C4A NAP sing 274 n y 
O3 PN NAP sing 275 n n 
PN O1N NAP doub 276 n n 
PN O2N NAP sing 277 n n 
PN O5D NAP sing 278 n n 
O5D C5D NAP sing 279 n n 
C5D C4D NAP sing 280 n n 
C5D H51N NAP sing 281 n n 
C5D H52N NAP sing 282 n n 
C4D O4D NAP sing 283 n n 
C4D C3D NAP sing 284 n n 
C4D H4D NAP sing 285 n n 
O4D C1D NAP sing 286 n n 
C3D O3D NAP sing 287 n n 
C3D C2D NAP sing 288 n n 
C3D H3D NAP sing 289 n n 
O3D HO3N NAP sing 290 n n 
C2D O2D NAP sing 291 n n 
C2D C1D NAP sing 292 n n 
C2D H2D NAP sing 293 n n 
O2D HO2N NAP sing 294 n n 
C1D N1N NAP sing 295 n n 
C1D H1D NAP sing 296 n n 
N1N C2N NAP sing 297 n y 
N1N C6N NAP doub 298 n y 
C2N C3N NAP doub 299 n y 
C2N H2N NAP sing 300 n n 
C3N C7N NAP sing 301 n n 
C3N C4N NAP sing 302 n y 
C7N O7N NAP doub 303 n n 
C7N N7N NAP sing 304 n n 
N7N H71N NAP sing 305 n n 
N7N H72N NAP sing 306 n n 
C4N C5N NAP doub 307 n y 
C4N H4N NAP sing 308 n n 
C5N C6N NAP sing 309 n y 
C5N H5N NAP sing 310 n n 
C6N H6N NAP sing 311 n n 
P2B O1X NAP doub 312 n n 
P2B O2X NAP sing 313 n n 
P2B O3X NAP sing 314 n n 
O2X HOP2 NAP sing 315 n n 
O3X HOP3 NAP sing 316 n n 
#
_atom_sites.entry_id                     2YDB 
_atom_sites.fract_transf_matrix[1][1]    0.023958 
_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]    0.021363 
_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]    0.009356 
_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 1379 1379 NAP NAP . 
C 3 HOH A 1 2001 2001 HOH HOH . 
C 3 HOH A 2 2002 2002 HOH HOH . 
C 3 HOH A 3 2003 2003 HOH HOH . 
C 3 HOH A 4 2004 2004 HOH HOH . 
C 3 HOH A 5 2005 2005 HOH HOH . 
C 3 HOH A 6 2006 2006 HOH HOH . 
C 3 HOH A 7 2007 2007 HOH HOH . 
C 3 HOH A 8 2008 2008 HOH HOH . 
C 3 HOH A 9 2009 2009 HOH HOH . 
C 3 HOH A 10 2010 2010 HOH HOH . 
C 3 HOH A 11 2011 2011 HOH HOH . 
C 3 HOH A 12 2012 2012 HOH HOH . 
C 3 HOH A 13 2013 2013 HOH HOH . 
C 3 HOH A 14 2014 2014 HOH HOH . 
C 3 HOH A 15 2015 2015 HOH HOH . 
C 3 HOH A 16 2016 2016 HOH HOH . 
C 3 HOH A 17 2017 2017 HOH HOH . 
C 3 HOH A 18 2018 2018 HOH HOH . 
C 3 HOH A 19 2019 2019 HOH HOH . 
C 3 HOH A 20 2020 2020 HOH HOH . 
C 3 HOH A 21 2021 2021 HOH HOH . 
C 3 HOH A 22 2022 2022 HOH HOH . 
C 3 HOH A 23 2023 2023 HOH HOH . 
C 3 HOH A 24 2024 2024 HOH HOH . 
C 3 HOH A 25 2025 2025 HOH HOH . 
C 3 HOH A 26 2026 2026 HOH HOH . 
C 3 HOH A 27 2027 2027 HOH HOH . 
C 3 HOH A 28 2028 2028 HOH HOH . 
C 3 HOH A 29 2029 2029 HOH HOH . 
C 3 HOH A 30 2030 2030 HOH HOH . 
C 3 HOH A 31 2031 2031 HOH HOH . 
C 3 HOH A 32 2032 2032 HOH HOH . 
C 3 HOH A 33 2033 2033 HOH HOH . 
C 3 HOH A 34 2034 2034 HOH HOH . 
C 3 HOH A 35 2035 2035 HOH HOH . 
C 3 HOH A 36 2036 2036 HOH HOH . 
C 3 HOH A 37 2037 2037 HOH HOH . 
C 3 HOH A 38 2038 2038 HOH HOH . 
C 3 HOH A 39 2039 2039 HOH HOH . 
C 3 HOH A 40 2040 2040 HOH HOH . 
C 3 HOH A 41 2041 2041 HOH HOH . 
C 3 HOH A 42 2042 2042 HOH HOH . 
C 3 HOH A 43 2043 2043 HOH HOH . 
C 3 HOH A 44 2044 2044 HOH HOH . 
C 3 HOH A 45 2045 2045 HOH HOH . 
C 3 HOH A 46 2046 2046 HOH HOH . 
C 3 HOH A 47 2047 2047 HOH HOH . 
C 3 HOH A 48 2048 2048 HOH HOH . 
C 3 HOH A 49 2049 2049 HOH HOH . 
C 3 HOH A 50 2050 2050 HOH HOH . 
C 3 HOH A 51 2051 2051 HOH HOH . 
C 3 HOH A 52 2052 2052 HOH HOH . 
C 3 HOH A 53 2053 2053 HOH HOH . 
C 3 HOH A 54 2054 2054 HOH HOH . 
C 3 HOH A 55 2055 2055 HOH HOH . 
C 3 HOH A 56 2056 2056 HOH HOH . 
C 3 HOH A 57 2057 2057 HOH HOH . 
C 3 HOH A 58 2058 2058 HOH HOH . 
C 3 HOH A 59 2059 2059 HOH HOH . 
C 3 HOH A 60 2060 2060 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 -4.956 2.661 -28.892 1 149.63 ? PA NAP 1379 A 1 
HETATM 2 O O1A NAP . . . B 2 -4.275 3.298 -30.042 1 149.39 ? O1A NAP 1379 A 1 
HETATM 3 O O2A NAP . . . B 2 -4.261 1.414 -28.494 1 148.97 ? O2A NAP 1379 A 1 
HETATM 4 O O5B NAP . . . B 2 -5.074 3.698 -27.659 1 95.38 ? O5B NAP 1379 A 1 
HETATM 5 C C5B NAP . . . B 2 -5.427 5.045 -27.899 1 92.34 ? C5B NAP 1379 A 1 
HETATM 6 C C4B NAP . . . B 2 -5.839 5.79 -26.627 1 86.8 ? C4B NAP 1379 A 1 
HETATM 7 O O4B NAP . . . B 2 -7.233 5.685 -26.398 1 86.37 ? O4B NAP 1379 A 1 
HETATM 8 C C3B NAP . . . B 2 -5.172 5.311 -25.344 1 83.53 ? C3B NAP 1379 A 1 
HETATM 9 O O3B NAP . . . B 2 -4.068 6.133 -25.042 1 78.98 ? O3B NAP 1379 A 1 
HETATM 10 C C2B NAP . . . B 2 -6.231 5.457 -24.265 1 84.82 ? C2B NAP 1379 A 1 
HETATM 11 O O2B NAP . . . B 2 -5.859 6.508 -23.411 1 83.99 ? O2B NAP 1379 A 1 
HETATM 12 C C1B NAP . . . B 2 -7.477 5.89 -25.017 1 85.8 ? C1B NAP 1379 A 1 
HETATM 13 N N9A NAP . . . B 2 -8.703 5.234 -24.509 1 86.9 ? N9A NAP 1379 A 1 
HETATM 14 C C8A NAP . . . B 2 -9.43 5.731 -23.461 1 89.34 ? C8A NAP 1379 A 1 
HETATM 15 N N7A NAP . . . B 2 -10.492 4.925 -23.24 1 92.09 ? N7A NAP 1379 A 1 
HETATM 16 C C5A NAP . . . B 2 -10.465 3.912 -24.137 1 88.26 ? C5A NAP 1379 A 1 
HETATM 17 C C6A NAP . . . B 2 -11.318 2.831 -24.339 1 84.42 ? C6A NAP 1379 A 1 
HETATM 18 N N6A NAP . . . B 2 -12.386 2.67 -23.558 1 79.88 ? N6A NAP 1379 A 1 
HETATM 19 N N1A NAP . . . B 2 -11.049 1.93 -25.352 1 85.97 ? N1A NAP 1379 A 1 
HETATM 20 C C2A NAP . . . B 2 -9.935 2.115 -26.149 1 85.31 ? C2A NAP 1379 A 1 
HETATM 21 N N3A NAP . . . B 2 -9.092 3.195 -25.939 1 84.11 ? N3A NAP 1379 A 1 
HETATM 22 C C4A NAP . . . B 2 -9.344 4.089 -24.947 1 86.07 ? C4A NAP 1379 A 1 
HETATM 23 O O3 NAP . . . B 2 -6.496 2.37 -29.262 1 130.39 ? O3 NAP 1379 A 1 
HETATM 24 P P2B NAP . . . B 2 -5.523 6.252 -21.855 1 102.95 ? P2B NAP 1379 A 1 
HETATM 25 O O1X NAP . . . B 2 -4.049 5.952 -21.71 1 99.54 ? O1X NAP 1379 A 1 
HETATM 26 O O2X NAP . . . B 2 -6.36 5.131 -21.295 1 101.88 ? O2X NAP 1379 A 1 
HETATM 27 O O3X NAP . . . B 2 -5.838 7.518 -21.103 1 105.63 ? O3X NAP 1379 A 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    15 
_model_server_stats.query_time_ms           299 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           27 
#