data_6PFD
#
_model_server_result.job_id            lVa7RsMNrJ1wG9glHSuSZA 
_model_server_result.datetime_utc      '2024-11-13 11:50:38' 
_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          6pfd 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":601}' 
#
_entry.id    6PFD 
#
_exptl.entry_id    6PFD 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              745.421 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' 
_entity.pdbx_number_of_molecules    5 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          95.05 
_cell.angle_gamma         90 
_cell.entry_id            6PFD 
_cell.length_a            213.033 
_cell.length_b            115.887 
_cell.length_c            220.808 
_cell.Z_PDB               20 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6PFD 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA dimeric 2 author_and_software_defined_assembly 1 
PISA dimeric 2 author_and_software_defined_assembly 2 
PISA dimeric 2 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,F,G,H,I,J,K,L,M 1 1 
C,D,N,O,P,Q,R,S,T,U 2 1 
E,V,W,X,Y 3 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 'crystal symmetry operation' 2_858 -x+3,y,-z+3 -1 0 0 0 1 0 0 0 -1 580.789092 0 659.852643 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 F N N 
? 2 J N N 
? 2 N N N 
? 2 R N N 
? 2 V N N 
#
_chem_comp.formula           'C21 H30 N7 O17 P3' 
_chem_comp.formula_weight    745.421 
_chem_comp.id                NDP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE' 
_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 NDP doub 292 n n 
PA O2A NDP sing 293 n n 
PA O5B NDP sing 294 n n 
PA O3 NDP sing 295 n n 
O2A HOA2 NDP sing 296 n n 
O5B C5B NDP sing 297 n n 
C5B C4B NDP sing 298 n n 
C5B H51A NDP sing 299 n n 
C5B H52A NDP sing 300 n n 
C4B O4B NDP sing 301 n n 
C4B C3B NDP sing 302 n n 
C4B H4B NDP sing 303 n n 
O4B C1B NDP sing 304 n n 
C3B O3B NDP sing 305 n n 
C3B C2B NDP sing 306 n n 
C3B H3B NDP sing 307 n n 
O3B HO3A NDP sing 308 n n 
C2B O2B NDP sing 309 n n 
C2B C1B NDP sing 310 n n 
C2B H2B NDP sing 311 n n 
O2B P2B NDP sing 312 n n 
C1B N9A NDP sing 313 n n 
C1B H1B NDP sing 314 n n 
N9A C8A NDP sing 315 n y 
N9A C4A NDP sing 316 n y 
C8A N7A NDP doub 317 n y 
C8A H8A NDP sing 318 n n 
N7A C5A NDP sing 319 n y 
C5A C6A NDP sing 320 n y 
C5A C4A NDP doub 321 n y 
C6A N6A NDP sing 322 n n 
C6A N1A NDP doub 323 n y 
N6A H61A NDP sing 324 n n 
N6A H62A NDP sing 325 n n 
N1A C2A NDP sing 326 n y 
C2A N3A NDP doub 327 n y 
C2A H2A NDP sing 328 n n 
N3A C4A NDP sing 329 n y 
O3 PN NDP sing 330 n n 
PN O1N NDP doub 331 n n 
PN O2N NDP sing 332 n n 
PN O5D NDP sing 333 n n 
O2N H21N NDP sing 334 n n 
O5D C5D NDP sing 335 n n 
C5D C4D NDP sing 336 n n 
C5D H51N NDP sing 337 n n 
C5D H52N NDP sing 338 n n 
C4D O4D NDP sing 339 n n 
C4D C3D NDP sing 340 n n 
C4D H4D NDP sing 341 n n 
O4D C1D NDP sing 342 n n 
C3D O3D NDP sing 343 n n 
C3D C2D NDP sing 344 n n 
C3D H3D NDP sing 345 n n 
O3D HO3N NDP sing 346 n n 
C2D O2D NDP sing 347 n n 
C2D C1D NDP sing 348 n n 
C2D H2D NDP sing 349 n n 
O2D HO2N NDP sing 350 n n 
C1D N1N NDP sing 351 n n 
C1D H1D NDP sing 352 n n 
N1N C2N NDP sing 353 n n 
N1N C6N NDP sing 354 n n 
C2N C3N NDP doub 355 n n 
C2N H2N NDP sing 356 n n 
C3N C7N NDP sing 357 n n 
C3N C4N NDP sing 358 n n 
C7N O7N NDP doub 359 n n 
C7N N7N NDP sing 360 n n 
N7N H71N NDP sing 361 n n 
N7N H72N NDP sing 362 n n 
C4N C5N NDP sing 363 n n 
C4N H41N NDP sing 364 n n 
C4N H42N NDP sing 365 n n 
C5N C6N NDP doub 366 n n 
C5N H5N NDP sing 367 n n 
C6N H6N NDP sing 368 n n 
P2B O1X NDP doub 369 n n 
P2B O2X NDP sing 370 n n 
P2B O3X NDP sing 371 n n 
O2X HOP2 NDP sing 372 n n 
O3X HOP3 NDP sing 373 n n 
#
_atom_sites.entry_id                     6PFD 
_atom_sites.fract_transf_matrix[1][1]    0.004694 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000414 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.008629 
_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]    0.004546 
_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
F 2 NDP A 1 601 601 NDP NDP . 
G 3 UFP A 1 602 602 UFP UFP . 
H 4 OEJ A 1 603 603 OEJ T11 . 
I 5 MTX A 1 604 604 MTX MTX . 
J 2 NDP B 1 601 601 NDP NDP . 
K 3 UFP B 1 602 602 UFP UFP . 
L 4 OEJ B 1 603 603 OEJ T11 . 
M 5 MTX B 1 604 604 MTX MTX . 
N 2 NDP C 1 601 601 NDP NDP . 
O 3 UFP C 1 602 602 UFP UFP . 
P 4 OEJ C 1 603 603 OEJ T11 . 
Q 5 MTX C 1 604 604 MTX MTX . 
R 2 NDP D 1 601 601 NDP NDP . 
S 3 UFP D 1 602 602 UFP UFP . 
T 4 OEJ D 1 603 603 OEJ T11 . 
U 5 MTX D 1 604 604 MTX MTX . 
V 2 NDP E 1 601 601 NDP NDP . 
W 3 UFP E 1 602 602 UFP UFP . 
X 4 OEJ E 1 603 603 OEJ T11 . 
Y 5 MTX E 1 604 604 MTX MTX . 
#
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 NDP . . . J 2 176.549 88.528 243.06 1 57.3 ? PA NDP 601 B 1 
HETATM 2 O O1A NDP . . . J 2 177.475 88.096 244.178 1 53.91 ? O1A NDP 601 B 1 
HETATM 3 O O2A NDP . . . J 2 177.161 88.195 241.729 1 67.47 ? O2A NDP 601 B 1 
HETATM 4 O O5B NDP . . . J 2 175.236 87.744 243.142 1 70.08 ? O5B NDP 601 B 1 
HETATM 5 C C5B NDP . . . J 2 174.455 87.77 244.303 1 74.88 ? C5B NDP 601 B 1 
HETATM 6 C C4B NDP . . . J 2 173.356 86.796 244.366 1 76.48 ? C4B NDP 601 B 1 
HETATM 7 O O4B NDP . . . J 2 173.878 85.52 244.669 1 63.86 ? O4B NDP 601 B 1 
HETATM 8 C C3B NDP . . . J 2 172.401 87.094 245.436 1 83.38 ? C3B NDP 601 B 1 
HETATM 9 O O3B NDP . . . J 2 171.398 87.95 245.013 1 73.75 ? O3B NDP 601 B 1 
HETATM 10 C C2B NDP . . . J 2 171.883 85.789 245.758 1 87.45 ? C2B NDP 601 B 1 
HETATM 11 O O2B NDP . . . J 2 170.97 85.359 244.79 1 80.51 ? O2B NDP 601 B 1 
HETATM 12 C C1B NDP . . . J 2 173.049 84.934 245.656 1 70.75 ? C1B NDP 601 B 1 
HETATM 13 N N9A NDP . . . J 2 173.723 84.84 246.904 1 81.99 ? N9A NDP 601 B 1 
HETATM 14 C C8A NDP . . . J 2 174.725 85.64 247.35 1 94.58 ? C8A NDP 601 B 1 
HETATM 15 N N7A NDP . . . J 2 175.111 85.237 248.576 1 93.62 ? N7A NDP 601 B 1 
HETATM 16 C C5A NDP . . . J 2 174.346 84.15 248.925 1 95.32 ? C5A NDP 601 B 1 
HETATM 17 C C6A NDP . . . J 2 174.285 83.309 250.061 1 86.73 ? C6A NDP 601 B 1 
HETATM 18 N N6A NDP . . . J 2 175.207 83.559 251.197 1 80.53 ? N6A NDP 601 B 1 
HETATM 19 N N1A NDP . . . J 2 173.39 82.284 250.106 1 81.53 ? N1A NDP 601 B 1 
HETATM 20 C C2A NDP . . . J 2 172.559 82.082 249.049 1 83.58 ? C2A NDP 601 B 1 
HETATM 21 N N3A NDP . . . J 2 172.579 82.847 247.954 1 81.99 ? N3A NDP 601 B 1 
HETATM 22 C C4A NDP . . . J 2 173.471 83.9 247.865 1 86.93 ? C4A NDP 601 B 1 
HETATM 23 O O3 NDP . . . J 2 176.251 90.099 243.126 1 83.23 ? O3 NDP 601 B 1 
HETATM 24 P PN NDP . . . J 2 177.394 91.207 243.254 1 81.65 ? PN NDP 601 B 1 
HETATM 25 O O1N NDP . . . J 2 176.794 92.613 243.42 1 59.64 ? O1N NDP 601 B 1 
HETATM 26 O O2N NDP . . . J 2 178.248 90.909 244.467 1 84.75 ? O2N NDP 601 B 1 
HETATM 27 O O5D NDP . . . J 2 178.3 91.184 241.91 1 66.03 ? O5D NDP 601 B 1 
HETATM 28 C C5D NDP . . . J 2 177.86 91.855 240.76 1 63.59 ? C5D NDP 601 B 1 
HETATM 29 C C4D NDP . . . J 2 178.739 92.876 240.218 1 74.95 ? C4D NDP 601 B 1 
HETATM 30 O O4D NDP . . . J 2 180.093 92.45 240.366 1 81.12 ? O4D NDP 601 B 1 
HETATM 31 C C3D NDP . . . J 2 178.524 93.059 238.777 1 70.5 ? C3D NDP 601 B 1 
HETATM 32 O O3D NDP . . . J 2 178.866 94.359 238.42 1 64.31 ? O3D NDP 601 B 1 
HETATM 33 C C2D NDP . . . J 2 179.459 92.158 238.201 1 71.27 ? C2D NDP 601 B 1 
HETATM 34 O O2D NDP . . . J 2 179.732 92.505 236.877 1 59.78 ? O2D NDP 601 B 1 
HETATM 35 C C1D NDP . . . J 2 180.625 92.363 239.087 1 83.92 ? C1D NDP 601 B 1 
HETATM 36 N N1N NDP . . . J 2 181.57 91.296 238.954 1 74.47 ? N1N NDP 601 B 1 
HETATM 37 C C2N NDP . . . J 2 182.868 91.613 238.803 1 62.76 ? C2N NDP 601 B 1 
HETATM 38 C C3N NDP . . . J 2 183.839 90.612 238.662 1 67.3 ? C3N NDP 601 B 1 
HETATM 39 C C7N NDP . . . J 2 185.291 91.02 238.493 1 62.5 ? C7N NDP 601 B 1 
HETATM 40 O O7N NDP . . . J 2 186.178 90.148 238.526 1 51.86 ? O7N NDP 601 B 1 
HETATM 41 N N7N NDP . . . J 2 185.648 92.397 238.295 1 55.55 ? N7N NDP 601 B 1 
HETATM 42 C C4N NDP . . . J 2 183.456 89.259 238.68 1 66.56 ? C4N NDP 601 B 1 
HETATM 43 C C5N NDP . . . J 2 182.096 88.967 238.838 1 64.45 ? C5N NDP 601 B 1 
HETATM 44 C C6N NDP . . . J 2 181.16 89.99 238.975 1 67.74 ? C6N NDP 601 B 1 
HETATM 45 P P2B NDP . . . J 2 169.44 85.314 245.085 1 63.81 ? P2B NDP 601 B 1 
HETATM 46 O O1X NDP . . . J 2 168.961 86.744 245.4 1 70.37 ? O1X NDP 601 B 1 
HETATM 47 O O2X NDP . . . J 2 168.746 84.779 243.903 1 54.22 ? O2X NDP 601 B 1 
HETATM 48 O O3X NDP . . . J 2 169.15 84.416 246.246 1 75.78 ? O3X NDP 601 B 1 
#
_model_server_stats.io_time_ms              15 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    26 
_model_server_stats.query_time_ms           287 
_model_server_stats.encode_time_ms          10 
_model_server_stats.element_count           48 
#