data_3UP4
#
_model_server_result.job_id            -GGPcHLE-lLes0S5-DEHsw 
_model_server_result.datetime_utc      '2024-11-29 13:55:13' 
_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          3up4 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":552}' 
#
_entry.id    3UP4 
#
_exptl.entry_id    3UP4 
_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    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            3UP4 
_cell.length_a            61.314 
_cell.length_b            66.2 
_cell.length_c            282.698 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3UP4 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
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 monomeric 1 software_defined_assembly 1 
PISA monomeric 1 software_defined_assembly 2 
? dimeric 2 author_defined_assembly 3 
#
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 
A,B,C,D,E,F,G,H 3 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 D N N 
? 3 F 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
disulf ? disulf1 A SG CYS 444 A CYS 444 1_555 A SG CYS 449 A CYS 449 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? 
disulf ? disulf2 B SG CYS 444 B CYS 444 1_555 B SG CYS 449 B CYS 449 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? 
#
_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 328 n n 
PA O2A NAP sing 329 n n 
PA O5B NAP sing 330 n n 
PA O3 NAP sing 331 n n 
O2A HOA2 NAP sing 332 n n 
O5B C5B NAP sing 333 n n 
C5B C4B NAP sing 334 n n 
C5B H51A NAP sing 335 n n 
C5B H52A NAP sing 336 n n 
C4B O4B NAP sing 337 n n 
C4B C3B NAP sing 338 n n 
C4B H4B NAP sing 339 n n 
O4B C1B NAP sing 340 n n 
C3B O3B NAP sing 341 n n 
C3B C2B NAP sing 342 n n 
C3B H3B NAP sing 343 n n 
O3B HO3A NAP sing 344 n n 
C2B O2B NAP sing 345 n n 
C2B C1B NAP sing 346 n n 
C2B H2B NAP sing 347 n n 
O2B P2B NAP sing 348 n n 
C1B N9A NAP sing 349 n n 
C1B H1B NAP sing 350 n n 
N9A C8A NAP sing 351 n y 
N9A C4A NAP sing 352 n y 
C8A N7A NAP doub 353 n y 
C8A H8A NAP sing 354 n n 
N7A C5A NAP sing 355 n y 
C5A C6A NAP sing 356 n y 
C5A C4A NAP doub 357 n y 
C6A N6A NAP sing 358 n n 
C6A N1A NAP doub 359 n y 
N6A H61A NAP sing 360 n n 
N6A H62A NAP sing 361 n n 
N1A C2A NAP sing 362 n y 
C2A N3A NAP doub 363 n y 
C2A H2A NAP sing 364 n n 
N3A C4A NAP sing 365 n y 
O3 PN NAP sing 366 n n 
PN O1N NAP doub 367 n n 
PN O2N NAP sing 368 n n 
PN O5D NAP sing 369 n n 
O5D C5D NAP sing 370 n n 
C5D C4D NAP sing 371 n n 
C5D H51N NAP sing 372 n n 
C5D H52N NAP sing 373 n n 
C4D O4D NAP sing 374 n n 
C4D C3D NAP sing 375 n n 
C4D H4D NAP sing 376 n n 
O4D C1D NAP sing 377 n n 
C3D O3D NAP sing 378 n n 
C3D C2D NAP sing 379 n n 
C3D H3D NAP sing 380 n n 
O3D HO3N NAP sing 381 n n 
C2D O2D NAP sing 382 n n 
C2D C1D NAP sing 383 n n 
C2D H2D NAP sing 384 n n 
O2D HO2N NAP sing 385 n n 
C1D N1N NAP sing 386 n n 
C1D H1D NAP sing 387 n n 
N1N C2N NAP sing 388 n y 
N1N C6N NAP doub 389 n y 
C2N C3N NAP doub 390 n y 
C2N H2N NAP sing 391 n n 
C3N C7N NAP sing 392 n n 
C3N C4N NAP sing 393 n y 
C7N O7N NAP doub 394 n n 
C7N N7N NAP sing 395 n n 
N7N H71N NAP sing 396 n n 
N7N H72N NAP sing 397 n n 
C4N C5N NAP doub 398 n y 
C4N H4N NAP sing 399 n n 
C5N C6N NAP sing 400 n y 
C5N H5N NAP sing 401 n n 
C6N H6N NAP sing 402 n n 
P2B O1X NAP doub 403 n n 
P2B O2X NAP sing 404 n n 
P2B O3X NAP sing 405 n n 
O2X HOP2 NAP sing 406 n n 
O3X HOP3 NAP sing 407 n n 
#
_atom_sites.entry_id                     3UP4 
_atom_sites.fract_transf_matrix[1][1]    0.016309 
_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]    0.015106 
_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]    0.003537 
_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 FAD A 1 551 551 FAD FAD . 
D 3 NAP A 1 552 552 NAP NAP . 
E 2 FAD B 1 551 551 FAD FAD . 
F 3 NAP B 1 552 552 NAP NAP . 
G 4 HOH A 1 546 6 HOH HOH . 
G 4 HOH A 2 547 7 HOH HOH . 
G 4 HOH A 3 548 10 HOH HOH . 
G 4 HOH A 4 549 12 HOH HOH . 
G 4 HOH A 5 550 13 HOH HOH . 
G 4 HOH A 6 553 19 HOH HOH . 
G 4 HOH A 7 554 22 HOH HOH . 
G 4 HOH A 8 555 25 HOH HOH . 
G 4 HOH A 9 556 27 HOH HOH . 
G 4 HOH A 10 557 29 HOH HOH . 
G 4 HOH A 11 558 30 HOH HOH . 
G 4 HOH A 12 559 31 HOH HOH . 
G 4 HOH A 13 560 32 HOH HOH . 
G 4 HOH A 14 561 35 HOH HOH . 
G 4 HOH A 15 562 38 HOH HOH . 
G 4 HOH A 16 563 41 HOH HOH . 
G 4 HOH A 17 564 46 HOH HOH . 
H 4 HOH B 1 546 1 HOH HOH . 
H 4 HOH B 2 547 2 HOH HOH . 
H 4 HOH B 3 548 3 HOH HOH . 
H 4 HOH B 4 549 4 HOH HOH . 
H 4 HOH B 5 550 5 HOH HOH . 
H 4 HOH B 6 553 8 HOH HOH . 
H 4 HOH B 7 554 9 HOH HOH . 
H 4 HOH B 8 555 11 HOH HOH . 
H 4 HOH B 9 556 14 HOH HOH . 
H 4 HOH B 10 557 15 HOH HOH . 
H 4 HOH B 11 558 16 HOH HOH . 
H 4 HOH B 12 559 17 HOH HOH . 
H 4 HOH B 13 560 18 HOH HOH . 
H 4 HOH B 14 561 20 HOH HOH . 
H 4 HOH B 15 562 21 HOH HOH . 
H 4 HOH B 16 563 23 HOH HOH . 
H 4 HOH B 17 564 24 HOH HOH . 
H 4 HOH B 18 565 26 HOH HOH . 
H 4 HOH B 19 566 28 HOH HOH . 
H 4 HOH B 20 567 33 HOH HOH . 
H 4 HOH B 21 568 34 HOH HOH . 
H 4 HOH B 22 569 36 HOH HOH . 
H 4 HOH B 23 570 37 HOH HOH . 
H 4 HOH B 24 571 39 HOH HOH . 
H 4 HOH B 25 572 40 HOH HOH . 
H 4 HOH B 26 573 42 HOH HOH . 
H 4 HOH B 27 574 43 HOH HOH . 
H 4 HOH B 28 575 44 HOH HOH . 
H 4 HOH B 29 576 45 HOH HOH . 
H 4 HOH B 30 577 47 HOH HOH . 
H 4 HOH B 31 578 48 HOH HOH . 
H 4 HOH B 32 579 49 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 . . . D 3 21.257 -12.832 -51.541 1 27.23 ? PA NAP 552 A 1 
HETATM 2 O O1A NAP . . . D 3 21.961 -11.591 -51.925 1 29.33 ? O1A NAP 552 A 1 
HETATM 3 O O2A NAP . . . D 3 20.765 -12.722 -50.168 1 27.16 ? O2A NAP 552 A 1 
HETATM 4 O O5B NAP . . . D 3 22.229 -14.095 -51.7 1 28.71 ? O5B NAP 552 A 1 
HETATM 5 C C5B NAP . . . D 3 22.986 -14.275 -52.877 1 29.49 ? C5B NAP 552 A 1 
HETATM 6 C C4B NAP . . . D 3 23.832 -15.535 -52.737 1 31.41 ? C4B NAP 552 A 1 
HETATM 7 O O4B NAP . . . D 3 24.636 -15.739 -53.895 1 31.51 ? O4B NAP 552 A 1 
HETATM 8 C C3B NAP . . . D 3 24.759 -15.383 -51.541 1 31.8 ? C3B NAP 552 A 1 
HETATM 9 O O3B NAP . . . D 3 24.921 -16.616 -50.885 1 31.89 ? O3B NAP 552 A 1 
HETATM 10 C C2B NAP . . . D 3 26.045 -14.987 -52.198 1 32.15 ? C2B NAP 552 A 1 
HETATM 11 O O2B NAP . . . D 3 27.125 -15.427 -51.445 1 32.2 ? O2B NAP 552 A 1 
HETATM 12 C C1B NAP . . . D 3 25.987 -15.764 -53.494 1 33.13 ? C1B NAP 552 A 1 
HETATM 13 N N9A NAP . . . D 3 26.881 -15.089 -54.431 1 35.88 ? N9A NAP 552 A 1 
HETATM 14 C C8A NAP . . . D 3 26.725 -13.85 -54.975 1 36.44 ? C8A NAP 552 A 1 
HETATM 15 N N7A NAP . . . D 3 27.783 -13.614 -55.768 1 37.39 ? N7A NAP 552 A 1 
HETATM 16 C C5A NAP . . . D 3 28.616 -14.669 -55.74 1 38.14 ? C5A NAP 552 A 1 
HETATM 17 C C6A NAP . . . D 3 29.833 -14.933 -56.365 1 39.41 ? C6A NAP 552 A 1 
HETATM 18 N N6A NAP . . . D 3 30.403 -14.05 -57.18 1 40.87 ? N6A NAP 552 A 1 
HETATM 19 N N1A NAP . . . D 3 30.466 -16.126 -56.127 1 40.51 ? N1A NAP 552 A 1 
HETATM 20 C C2A NAP . . . D 3 29.89 -17.052 -55.269 1 41.25 ? C2A NAP 552 A 1 
HETATM 21 N N3A NAP . . . D 3 28.681 -16.787 -54.649 1 40.48 ? N3A NAP 552 A 1 
HETATM 22 C C4A NAP . . . D 3 28.059 -15.604 -54.886 1 38.12 ? C4A NAP 552 A 1 
HETATM 23 O O3 NAP . . . D 3 20.138 -13.043 -52.655 1 27.09 ? O3 NAP 552 A 1 
HETATM 24 P PN NAP . . . D 3 18.786 -13.861 -52.576 1 27.79 ? PN NAP 552 A 1 
HETATM 25 O O1N NAP . . . D 3 19.09 -15.215 -52.084 1 28.43 ? O1N NAP 552 A 1 
HETATM 26 O O2N NAP . . . D 3 17.896 -13.682 -53.752 1 26.84 ? O2N NAP 552 A 1 
HETATM 27 O O5D NAP . . . D 3 18.25 -12.944 -51.393 1 32.87 ? O5D NAP 552 A 1 
HETATM 28 C C5D NAP . . . D 3 17.973 -11.591 -51.655 1 38.17 ? C5D NAP 552 A 1 
HETATM 29 C C4D NAP . . . D 3 16.753 -11.136 -50.857 1 42.51 ? C4D NAP 552 A 1 
HETATM 30 O O4D NAP . . . D 3 15.555 -11.471 -51.529 1 43.7 ? O4D NAP 552 A 1 
HETATM 31 C C3D NAP . . . D 3 16.6 -11.694 -49.432 1 43.47 ? C3D NAP 552 A 1 
HETATM 32 O O3D NAP . . . D 3 17.41 -11.066 -48.473 1 42.39 ? O3D NAP 552 A 1 
HETATM 33 C C2D NAP . . . D 3 15.119 -11.494 -49.155 1 45.38 ? C2D NAP 552 A 1 
HETATM 34 O O2D NAP . . . D 3 14.793 -10.259 -48.546 1 44.29 ? O2D NAP 552 A 1 
HETATM 35 C C1D NAP . . . D 3 14.517 -11.587 -50.561 1 47.54 ? C1D NAP 552 A 1 
HETATM 36 N N1N NAP . . . D 3 13.861 -12.91 -50.661 1 51.68 ? N1N NAP 552 A 1 
HETATM 37 C C2N NAP . . . D 3 12.861 -13.208 -49.753 1 54.2 ? C2N NAP 552 A 1 
HETATM 38 C C3N NAP . . . D 3 12.206 -14.442 -49.801 1 54.74 ? C3N NAP 552 A 1 
HETATM 39 C C7N NAP . . . D 3 11.322 -14.829 -48.659 1 54.63 ? C7N NAP 552 A 1 
HETATM 40 O O7N NAP . . . D 3 11.811 -15.769 -47.716 1 55.39 ? O7N NAP 552 A 1 
HETATM 41 N N7N NAP . . . D 3 10.121 -14.249 -48.578 1 54.01 ? N7N NAP 552 A 1 
HETATM 42 C C4N NAP . . . D 3 12.584 -15.375 -50.767 1 54.15 ? C4N NAP 552 A 1 
HETATM 43 C C5N NAP . . . D 3 13.608 -15.07 -51.672 1 53.07 ? C5N NAP 552 A 1 
HETATM 44 C C6N NAP . . . D 3 14.245 -13.83 -51.612 1 51.97 ? C6N NAP 552 A 1 
HETATM 45 P P2B NAP . . . D 3 27.996 -14.384 -50.601 1 32.74 ? P2B NAP 552 A 1 
HETATM 46 O O1X NAP . . . D 3 27.269 -14.083 -49.303 1 33.35 ? O1X NAP 552 A 1 
HETATM 47 O O2X NAP . . . D 3 29.35 -14.989 -50.319 1 33.89 ? O2X NAP 552 A 1 
HETATM 48 O O3X NAP . . . D 3 28.219 -13.12 -51.393 1 33.48 ? O3X NAP 552 A 1 
#
_model_server_stats.io_time_ms              22 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    20 
_model_server_stats.query_time_ms           313 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           48 
#