data_1YKF
#
_model_server_result.job_id            g_qTO97jStYMoR5XXYyHZA 
_model_server_result.datetime_utc      '2024-11-15 11:36:47' 
_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          1ykf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":353}' 
#
_entry.id    1YKF 
#
_exptl.entry_id    1YKF 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              743.405 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' 
_entity.pdbx_number_of_molecules    4 
_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         120 
_cell.entry_id            1YKF 
_cell.length_a            80.614 
_cell.length_b            80.614 
_cell.length_c            400.335 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1YKF 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        170 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 65' 
#
_pdbx_struct_assembly.method_details        PISA 
_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,I,J,K,L,M,N,O,P 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 F N N 
? 3 H N N 
? 3 J N N 
? 3 L 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
metalc ? metalc1 A SG CYS 37 A CYS 37 1_555 E ZN ZN . A ZN 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.619 ? 
metalc ? metalc2 A NE2 HIS 59 A HIS 59 1_555 E ZN ZN . A ZN 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? 
metalc ? metalc3 A OD2 ASP 150 A ASP 150 1_555 E ZN ZN . A ZN 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? 
metalc ? metalc4 B SG CYS 37 B CYS 37 1_555 G ZN ZN . B ZN 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.923 ? 
metalc ? metalc5 B NE2 HIS 59 B HIS 59 1_555 G ZN ZN . B ZN 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? 
metalc ? metalc6 B OD2 ASP 150 B ASP 150 1_555 G ZN ZN . B ZN 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.308 ? 
metalc ? metalc7 C SG CYS 37 C CYS 37 1_555 I ZN ZN . C ZN 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.861 ? 
metalc ? metalc8 C NE2 HIS 59 C HIS 59 1_555 I ZN ZN . C ZN 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
metalc ? metalc9 C OD2 ASP 150 C ASP 150 1_555 I ZN ZN . C ZN 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? 
metalc ? metalc10 D SG CYS 37 D CYS 37 1_555 K ZN ZN . D ZN 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.729 ? 
metalc ? metalc11 D NE2 HIS 59 D HIS 59 1_555 K ZN ZN . D ZN 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? 
metalc ? metalc12 D OD2 ASP 150 D ASP 150 1_555 K ZN ZN . D ZN 354 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.472 ? 
#
_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                     1YKF 
_atom_sites.fract_transf_matrix[1][1]    0.012405 
_atom_sites.fract_transf_matrix[1][2]    0.007162 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014324 
_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]    0.002498 
_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
E 2 ZN A 1 354 354 ZN ZN . 
F 3 NAP A 1 353 353 NAP NAP . 
G 2 ZN B 1 354 354 ZN ZN . 
H 3 NAP B 1 353 353 NAP NAP . 
I 2 ZN C 1 354 354 ZN ZN . 
J 3 NAP C 1 353 353 NAP NAP . 
K 2 ZN D 1 354 354 ZN ZN . 
L 3 NAP D 1 353 353 NAP NAP . 
M 4 HOH A 1 355 1 HOH HOH . 
M 4 HOH A 2 356 2 HOH HOH . 
M 4 HOH A 3 357 3 HOH HOH . 
M 4 HOH A 4 358 4 HOH HOH . 
M 4 HOH A 5 359 5 HOH HOH . 
M 4 HOH A 6 360 6 HOH HOH . 
M 4 HOH A 7 361 7 HOH HOH . 
M 4 HOH A 8 362 8 HOH HOH . 
M 4 HOH A 9 363 9 HOH HOH . 
M 4 HOH A 10 364 13 HOH HOH . 
N 4 HOH B 1 355 10 HOH HOH . 
N 4 HOH B 2 356 11 HOH HOH . 
N 4 HOH B 3 357 12 HOH HOH . 
N 4 HOH B 4 358 14 HOH HOH . 
N 4 HOH B 5 359 15 HOH HOH . 
N 4 HOH B 6 360 16 HOH HOH . 
N 4 HOH B 7 361 17 HOH HOH . 
N 4 HOH B 8 362 18 HOH HOH . 
N 4 HOH B 9 363 19 HOH HOH . 
N 4 HOH B 10 364 20 HOH HOH . 
O 4 HOH C 1 355 21 HOH HOH . 
O 4 HOH C 2 356 22 HOH HOH . 
O 4 HOH C 3 357 23 HOH HOH . 
O 4 HOH C 4 358 25 HOH HOH . 
O 4 HOH C 5 359 26 HOH HOH . 
O 4 HOH C 6 360 27 HOH HOH . 
O 4 HOH C 7 361 28 HOH HOH . 
O 4 HOH C 8 362 29 HOH HOH . 
O 4 HOH C 9 363 30 HOH HOH . 
O 4 HOH C 10 364 31 HOH HOH . 
O 4 HOH C 11 365 32 HOH HOH . 
P 4 HOH D 1 355 24 HOH HOH . 
P 4 HOH D 2 356 33 HOH HOH . 
P 4 HOH D 3 357 34 HOH HOH . 
P 4 HOH D 4 358 35 HOH HOH . 
P 4 HOH D 5 359 36 HOH HOH . 
P 4 HOH D 6 360 37 HOH HOH . 
P 4 HOH D 7 361 38 HOH HOH . 
P 4 HOH D 8 362 39 HOH HOH . 
P 4 HOH D 9 363 40 HOH HOH . 
P 4 HOH D 10 364 41 HOH HOH . 
P 4 HOH D 11 365 42 HOH HOH . 
P 4 HOH D 12 366 43 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 . . . L 3 9.811 9.346 2.299 1 120.14 ? PA NAP 353 D 1 
HETATM 2 O O1A NAP . . . L 3 9.253 10.447 1.475 1 118.4 ? O1A NAP 353 D 1 
HETATM 3 O O2A NAP . . . L 3 8.871 8.465 3.031 1 121.83 ? O2A NAP 353 D 1 
HETATM 4 O O5B NAP . . . L 3 10.784 9.941 3.433 1 113.54 ? O5B NAP 353 D 1 
HETATM 5 C C5B NAP . . . L 3 10.432 11.165 4.076 1 107.37 ? C5B NAP 353 D 1 
HETATM 6 C C4B NAP . . . L 3 11 11.131 5.479 1 103.43 ? C4B NAP 353 D 1 
HETATM 7 O O4B NAP . . . L 3 11.033 12.484 5.966 1 103.29 ? O4B NAP 353 D 1 
HETATM 8 C C3B NAP . . . L 3 10.123 10.325 6.439 1 105.15 ? C3B NAP 353 D 1 
HETATM 9 O O3B NAP . . . L 3 10.837 9.768 7.547 1 103.14 ? O3B NAP 353 D 1 
HETATM 10 C C2B NAP . . . L 3 9.137 11.361 6.957 1 106.37 ? C2B NAP 353 D 1 
HETATM 11 O O2B NAP . . . L 3 8.561 11.039 8.239 1 102.43 ? O2B NAP 353 D 1 
HETATM 12 C C1B NAP . . . L 3 9.782 12.687 6.638 1 103.25 ? C1B NAP 353 D 1 
HETATM 13 N N9A NAP . . . L 3 9.222 14.023 6.94 1 102.43 ? N9A NAP 353 D 1 
HETATM 14 C C8A NAP . . . L 3 8.102 14.552 6.42 1 101.32 ? C8A NAP 353 D 1 
HETATM 15 N N7A NAP . . . L 3 7.907 15.805 6.852 1 105.57 ? N7A NAP 353 D 1 
HETATM 16 C C5A NAP . . . L 3 8.937 16.012 7.656 1 107.73 ? C5A NAP 353 D 1 
HETATM 17 C C6A NAP . . . L 3 9.164 17.189 8.354 1 109.01 ? C6A NAP 353 D 1 
HETATM 18 N N6A NAP . . . L 3 8.321 18.212 8.258 1 108.61 ? N6A NAP 353 D 1 
HETATM 19 N N1A NAP . . . L 3 10.272 17.226 9.124 1 109.27 ? N1A NAP 353 D 1 
HETATM 20 C C2A NAP . . . L 3 11.099 16.176 9.201 1 109.08 ? C2A NAP 353 D 1 
HETATM 21 N N3A NAP . . . L 3 10.868 15.044 8.53 1 108.52 ? N3A NAP 353 D 1 
HETATM 22 C C4A NAP . . . L 3 9.78 14.93 7.738 1 106.38 ? C4A NAP 353 D 1 
HETATM 23 O O3 NAP . . . L 3 10.792 8.409 1.416 1 122.76 ? O3 NAP 353 D 1 
HETATM 24 P PN NAP . . . L 3 12.261 8.467 0.744 1 124.77 ? PN NAP 353 D 1 
HETATM 25 O O1N NAP . . . L 3 12.246 7.633 -0.481 1 123.02 ? O1N NAP 353 D 1 
HETATM 26 O O2N NAP . . . L 3 13.272 8.13 1.78 1 119.68 ? O2N NAP 353 D 1 
HETATM 27 O O5D NAP . . . L 3 12.431 10.006 0.29 1 126.83 ? O5D NAP 353 D 1 
HETATM 28 C C5D NAP . . . L 3 13.688 10.511 -0.186 1 123.66 ? C5D NAP 353 D 1 
HETATM 29 C C4D NAP . . . L 3 13.526 11.844 -0.913 1 122.86 ? C4D NAP 353 D 1 
HETATM 30 O O4D NAP . . . L 3 14.696 12.03 -1.739 1 123.68 ? O4D NAP 353 D 1 
HETATM 31 C C3D NAP . . . L 3 12.357 11.877 -1.895 1 123.8 ? C3D NAP 353 D 1 
HETATM 32 O O3D NAP . . . L 3 11.894 13.207 -2.204 1 121.01 ? O3D NAP 353 D 1 
HETATM 33 C C2D NAP . . . L 3 12.945 11.187 -3.118 1 123.15 ? C2D NAP 353 D 1 
HETATM 34 O O2D NAP . . . L 3 12.222 11.643 -4.263 1 124.49 ? O2D NAP 353 D 1 
HETATM 35 C C1D NAP . . . L 3 14.374 11.703 -3.112 1 121.43 ? C1D NAP 353 D 1 
HETATM 36 N N1N NAP . . . L 3 15.29 10.736 -3.763 1 115.99 ? N1N NAP 353 D 1 
HETATM 37 C C2N NAP . . . L 3 15.507 10.793 -5.156 1 109.46 ? C2N NAP 353 D 1 
HETATM 38 C C3N NAP . . . L 3 16.354 9.864 -5.76 1 103.68 ? C3N NAP 353 D 1 
HETATM 39 C C7N NAP . . . L 3 16.603 9.841 -7.273 1 98.45 ? C7N NAP 353 D 1 
HETATM 40 O O7N NAP . . . L 3 17.175 8.885 -7.786 1 92.91 ? O7N NAP 353 D 1 
HETATM 41 N N7N NAP . . . L 3 16.166 10.87 -7.979 1 95.73 ? N7N NAP 353 D 1 
HETATM 42 C C4N NAP . . . L 3 16.972 8.903 -4.965 1 104.73 ? C4N NAP 353 D 1 
HETATM 43 C C5N NAP . . . L 3 16.767 8.837 -3.591 1 108.06 ? C5N NAP 353 D 1 
HETATM 44 C C6N NAP . . . L 3 15.923 9.756 -2.982 1 112.32 ? C6N NAP 353 D 1 
HETATM 45 P P2B NAP . . . L 3 7.45 9.884 8.415 1 96.91 ? P2B NAP 353 D 1 
HETATM 46 O O1X NAP . . . L 3 6.217 10.68 8.603 1 89.12 ? O1X NAP 353 D 1 
HETATM 47 O O2X NAP . . . L 3 7.959 9.193 9.626 1 94.06 ? O2X NAP 353 D 1 
HETATM 48 O O3X NAP . . . L 3 7.465 9.048 7.193 1 93.94 ? O3X NAP 353 D 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    27 
_model_server_stats.query_time_ms           315 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           48 
#