data_4XVD
#
_model_server_result.job_id            W15mFDfmt-Ubyaq5-fAmrg 
_model_server_result.datetime_utc      '2024-12-25 06:03:22' 
_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          4xvd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":401}' 
#
_entry.id    4XVD 
#
_exptl.entry_id    4XVD 
_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    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            4XVD 
_cell.length_a            145.795 
_cell.length_b            145.795 
_cell.length_c            74.287 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4XVD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        79 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 4' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
? monomeric 1 author_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,G 1 1 
B,E,F,H 2 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 C N N 
? 2 E N 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                     4XVD 
_atom_sites.fract_transf_matrix[1][1]    0.006859 
_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]    0.006859 
_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]    0.013461 
_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 NAP A 1 401 1 NAP NAP . 
D 3 WDV A 1 402 1 WDV WDV . 
E 2 NAP B 1 401 1 NAP NAP . 
F 3 WDV B 1 402 1 WDV WDV . 
G 4 HOH A 1 501 2 HOH HOH . 
G 4 HOH A 2 502 1 HOH HOH . 
G 4 HOH A 3 503 3 HOH HOH . 
G 4 HOH A 4 504 4 HOH HOH . 
G 4 HOH A 5 505 5 HOH HOH . 
G 4 HOH A 6 506 6 HOH HOH . 
G 4 HOH A 7 507 10 HOH HOH . 
G 4 HOH A 8 508 11 HOH HOH . 
G 4 HOH A 9 509 12 HOH HOH . 
G 4 HOH A 10 510 13 HOH HOH . 
H 4 HOH B 1 501 7 HOH HOH . 
H 4 HOH B 2 502 8 HOH HOH . 
H 4 HOH B 3 503 9 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 . . . C 2 156.646 33.044 31.813 1 24.06 ? PA NAP 401 A 1 
HETATM 2 O O1A NAP . . . C 2 155.854 31.8 31.915 1 23.53 ? O1A NAP 401 A 1 
HETATM 3 O O2A NAP . . . C 2 156.828 33.973 32.955 1 22.16 ? O2A NAP 401 A 1 
HETATM 4 O O5B NAP . . . C 2 155.972 33.889 30.631 1 23.67 ? O5B NAP 401 A 1 
HETATM 5 C C5B NAP . . . C 2 155.764 33.177 29.446 1 22.33 ? C5B NAP 401 A 1 
HETATM 6 C C4B NAP . . . C 2 155.183 34.049 28.385 1 22.71 ? C4B NAP 401 A 1 
HETATM 7 O O4B NAP . . . C 2 154.044 34.748 28.843 1 22.9 ? O4B NAP 401 A 1 
HETATM 8 C C3B NAP . . . C 2 156.159 35.085 27.941 1 22.68 ? C3B NAP 401 A 1 
HETATM 9 O O3B NAP . . . C 2 156.706 34.609 26.743 1 22.72 ? O3B NAP 401 A 1 
HETATM 10 C C2B NAP . . . C 2 155.304 36.296 27.658 1 22.92 ? C2B NAP 401 A 1 
HETATM 11 O O2B NAP . . . C 2 155.38 36.723 26.297 1 22.92 ? O2B NAP 401 A 1 
HETATM 12 C C1B NAP . . . C 2 153.901 35.863 27.979 1 22.04 ? C1B NAP 401 A 1 
HETATM 13 N N9A NAP . . . C 2 153.275 36.894 28.751 1 21.4 ? N9A NAP 401 A 1 
HETATM 14 C C8A NAP . . . C 2 153.881 37.576 29.751 1 21.24 ? C8A NAP 401 A 1 
HETATM 15 N N7A NAP . . . C 2 153.078 38.461 30.277 1 20.78 ? N7A NAP 401 A 1 
HETATM 16 C C5A NAP . . . C 2 151.913 38.338 29.585 1 21 ? C5A NAP 401 A 1 
HETATM 17 C C6A NAP . . . C 2 150.726 39.013 29.7 1 21.02 ? C6A NAP 401 A 1 
HETATM 18 N N6A NAP . . . C 2 150.555 39.999 30.653 1 21.38 ? N6A NAP 401 A 1 
HETATM 19 N N1A NAP . . . C 2 149.752 38.669 28.872 1 21.38 ? N1A NAP 401 A 1 
HETATM 20 C C2A NAP . . . C 2 149.974 37.707 27.984 1 21.92 ? C2A NAP 401 A 1 
HETATM 21 N N3A NAP . . . C 2 151.071 36.993 27.776 1 22.9 ? N3A NAP 401 A 1 
HETATM 22 C C4A NAP . . . C 2 152.014 37.369 28.63 1 21.73 ? C4A NAP 401 A 1 
HETATM 23 O O3 NAP . . . C 2 158.11 32.77 31.221 1 24.17 ? O3 NAP 401 A 1 
HETATM 24 P PN NAP . . . C 2 159.42 31.994 31.68 1 24.82 ? PN NAP 401 A 1 
HETATM 25 O O1N NAP . . . C 2 159.236 30.54 31.518 1 25.97 ? O1N NAP 401 A 1 
HETATM 26 O O2N NAP . . . C 2 160.561 32.685 31.063 1 24.76 ? O2N NAP 401 A 1 
HETATM 27 O O5D NAP . . . C 2 159.572 32.327 33.221 1 22.57 ? O5D NAP 401 A 1 
HETATM 28 C C5D NAP . . . C 2 160.162 33.587 33.43 1 21.38 ? C5D NAP 401 A 1 
HETATM 29 C C4D NAP . . . C 2 161.42 33.505 34.218 1 20.05 ? C4D NAP 401 A 1 
HETATM 30 O O4D NAP . . . C 2 161.478 32.293 34.911 1 19.33 ? O4D NAP 401 A 1 
HETATM 31 C C3D NAP . . . C 2 162.565 33.352 33.297 1 20.15 ? C3D NAP 401 A 1 
HETATM 32 O O3D NAP . . . C 2 162.908 34.596 32.79 1 21.42 ? O3D NAP 401 A 1 
HETATM 33 C C2D NAP . . . C 2 163.587 32.935 34.287 1 19.98 ? C2D NAP 401 A 1 
HETATM 34 O O2D NAP . . . C 2 164.061 34.089 34.944 1 19.28 ? O2D NAP 401 A 1 
HETATM 35 C C1D NAP . . . C 2 162.82 32.125 35.287 1 19.35 ? C1D NAP 401 A 1 
HETATM 36 N N1N NAP . . . C 2 163.077 30.751 35.008 1 19.22 ? N1N NAP 401 A 1 
HETATM 37 C C2N NAP . . . C 2 163.886 30.037 35.767 1 19.25 ? C2N NAP 401 A 1 
HETATM 38 C C3N NAP . . . C 2 164.086 28.72 35.434 1 18.51 ? C3N NAP 401 A 1 
HETATM 39 C C7N NAP . . . C 2 164.934 27.93 36.293 1 17.83 ? C7N NAP 401 A 1 
HETATM 40 O O7N NAP . . . C 2 165.378 26.863 35.961 1 17.31 ? O7N NAP 401 A 1 
HETATM 41 N N7N NAP . . . C 2 165.061 28.469 37.52 1 17.33 ? N7N NAP 401 A 1 
HETATM 42 C C4N NAP . . . C 2 163.48 28.137 34.352 1 18.83 ? C4N NAP 401 A 1 
HETATM 43 C C5N NAP . . . C 2 162.66 28.918 33.581 1 19.42 ? C5N NAP 401 A 1 
HETATM 44 C C6N NAP . . . C 2 162.479 30.224 33.954 1 19.75 ? C6N NAP 401 A 1 
HETATM 45 P P2B NAP . . . C 2 155.986 38.165 25.906 1 22.08 ? P2B NAP 401 A 1 
HETATM 46 O O1X NAP . . . C 2 157.411 37.993 26.167 1 20.65 ? O1X NAP 401 A 1 
HETATM 47 O O2X NAP . . . C 2 155.621 38.217 24.479 1 21.83 ? O2X NAP 401 A 1 
HETATM 48 O O3X NAP . . . C 2 155.387 39.239 26.707 1 22.24 ? O3X NAP 401 A 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           21 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           498 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           48 
#