data_4PZT
#
_model_server_result.job_id            9zZ416y1wZR53N0rR48WSg 
_model_server_result.datetime_utc      '2024-11-16 14:36:02' 
_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          4pzt 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"B","auth_seq_id":1701}' 
#
_entry.id    4PZT 
#
_exptl.entry_id    4PZT 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              823.597 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R)-3-HYDROXY-2,2-DIMETHYL-4-OXO-4-{[3-OXO-3-({2-[(2-OXOPROPYL)THIO]ETHYL}AMINO)PROPYL]AMINO}BUTYL DIHYDROGEN DIPHOSPHATE' 
_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            4PZT 
_cell.length_a            63.681 
_cell.length_b            63.681 
_cell.length_c            104.122 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4PZT 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        78 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43' 
#
_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,D,E,F 
_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           'C24 H40 N7 O17 P3 S' 
_chem_comp.formula_weight    823.597 
_chem_comp.id                SOP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-4-HYDROXY-3-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL (3R)-3-HYDROXY-2,2-DIMETHYL-4-OXO-4-{[3-OXO-3-({2-[(2-OXOPROPYL)THIO]ETHYL}AMINO)PROPYL]AMINO}BUTYL DIHYDROGEN DIPHOSPHATE' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'S-(2-OXOPROPYL)-COENZYME A' 
#
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
N6 C6 SOP sing 299 n n 
N6 HN61 SOP sing 300 n n 
N6 HN62 SOP sing 301 n n 
C6 N1 SOP sing 302 n y 
C6 C5 SOP doub 303 n y 
N1 C2 SOP doub 304 n y 
C2 N3 SOP sing 305 n y 
C2 H2 SOP sing 306 n n 
N3 C4 SOP doub 307 n y 
C4 C5 SOP sing 308 n y 
C4 N9 SOP sing 309 n y 
C5 N7 SOP sing 310 n y 
N7 C8 SOP doub 311 n y 
C8 N9 SOP sing 312 n y 
C8 H8 SOP sing 313 n n 
N9 C1' SOP sing 314 n n 
C1' O4' SOP sing 315 n n 
C1' C2' SOP sing 316 n n 
C1' H1' SOP sing 317 n n 
O4' C4' SOP sing 318 n n 
C2' O2' SOP sing 319 n n 
C2' C3' SOP sing 320 n n 
C2' H2' SOP sing 321 n n 
O2' HO2' SOP sing 322 n n 
C3' O3' SOP sing 323 n n 
C3' C4' SOP sing 324 n n 
C3' H3' SOP sing 325 n n 
O3' P3 SOP sing 326 n n 
P3 O32 SOP sing 327 n n 
P3 O33 SOP sing 328 n n 
P3 O31 SOP doub 329 n n 
O32 HO32 SOP sing 330 n n 
O33 HO33 SOP sing 331 n n 
C4' C5' SOP sing 332 n n 
C4' H4' SOP sing 333 n n 
C5' O5' SOP sing 334 n n 
C5' "H5'1" SOP sing 335 n n 
C5' "H5'2" SOP sing 336 n n 
O5' P1 SOP sing 337 n n 
P1 O11 SOP sing 338 n n 
P1 O12 SOP doub 339 n n 
P1 O6 SOP sing 340 n n 
O11 HO11 SOP sing 341 n n 
O6 P2 SOP sing 342 n n 
P2 O21 SOP sing 343 n n 
P2 O22 SOP doub 344 n n 
P2 O7 SOP sing 345 n n 
O21 HO21 SOP sing 346 n n 
O7 CP9 SOP sing 347 n n 
CP9 CP8 SOP sing 348 n n 
CP9 HP91 SOP sing 349 n n 
CP9 HP92 SOP sing 350 n n 
CP8 CPB SOP sing 351 n n 
CP8 CPA SOP sing 352 n n 
CP8 CP7 SOP sing 353 n n 
CPB HPB1 SOP sing 354 n n 
CPB HPB2 SOP sing 355 n n 
CPB HPB3 SOP sing 356 n n 
CPA HPA1 SOP sing 357 n n 
CPA HPA2 SOP sing 358 n n 
CPA HPA3 SOP sing 359 n n 
CP7 OP3 SOP sing 360 n n 
CP7 CP6 SOP sing 361 n n 
CP7 HP7 SOP sing 362 n n 
OP3 HOP3 SOP sing 363 n n 
CP6 OP2 SOP doub 364 n n 
CP6 NP2 SOP sing 365 n n 
NP2 CP5 SOP sing 366 n n 
NP2 HNP2 SOP sing 367 n n 
CP5 CP4 SOP sing 368 n n 
CP5 HP51 SOP sing 369 n n 
CP5 HP52 SOP sing 370 n n 
CP4 CP3 SOP sing 371 n n 
CP4 HP41 SOP sing 372 n n 
CP4 HP42 SOP sing 373 n n 
CP3 OP1 SOP doub 374 n n 
CP3 NP1 SOP sing 375 n n 
NP1 CP2 SOP sing 376 n n 
NP1 HNP1 SOP sing 377 n n 
CP2 CP1 SOP sing 378 n n 
CP2 HP21 SOP sing 379 n n 
CP2 HP22 SOP sing 380 n n 
CP1 S SOP sing 381 n n 
CP1 HP11 SOP sing 382 n n 
CP1 HP12 SOP sing 383 n n 
S CA1 SOP sing 384 n n 
CA1 CA2 SOP sing 385 n n 
CA1 HA11 SOP sing 386 n n 
CA1 HA12 SOP sing 387 n n 
CA2 OA1 SOP doub 388 n n 
CA2 CA3 SOP sing 389 n n 
CA3 HA31 SOP sing 390 n n 
CA3 HA32 SOP sing 391 n n 
CA3 HA33 SOP sing 392 n n 
#
_atom_sites.entry_id                     4PZT 
_atom_sites.fract_transf_matrix[1][1]    0.015703 
_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]    0.015703 
_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]    0.009604 
_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 SOP A 1 1701 700 SOP O1A . 
C 3 DMS A 1 1702 501 DMS DMS . 
D 3 DMS A 1 1703 1 DMS DMS . 
E 3 DMS A 1 1704 1 DMS DMS . 
F 4 HOH A 1 1801 1 HOH HOH . 
F 4 HOH A 2 1802 2 HOH HOH . 
F 4 HOH A 3 1803 3 HOH HOH . 
F 4 HOH A 4 1804 4 HOH HOH . 
F 4 HOH A 5 1805 5 HOH HOH . 
F 4 HOH A 6 1806 6 HOH HOH . 
F 4 HOH A 7 1807 7 HOH HOH . 
F 4 HOH A 8 1808 8 HOH HOH . 
F 4 HOH A 9 1809 9 HOH HOH . 
F 4 HOH A 10 1810 10 HOH HOH . 
F 4 HOH A 11 1811 11 HOH HOH . 
F 4 HOH A 12 1812 12 HOH HOH . 
F 4 HOH A 13 1813 13 HOH HOH . 
F 4 HOH A 14 1814 14 HOH HOH . 
F 4 HOH A 15 1815 15 HOH HOH . 
F 4 HOH A 16 1816 16 HOH HOH . 
F 4 HOH A 17 1817 17 HOH HOH . 
F 4 HOH A 18 1818 18 HOH HOH . 
F 4 HOH A 19 1819 19 HOH HOH . 
F 4 HOH A 20 1820 20 HOH HOH . 
F 4 HOH A 21 1821 21 HOH HOH . 
F 4 HOH A 22 1822 22 HOH HOH . 
F 4 HOH A 23 1823 23 HOH HOH . 
F 4 HOH A 24 1824 24 HOH HOH . 
F 4 HOH A 25 1825 25 HOH HOH . 
F 4 HOH A 26 1826 26 HOH HOH . 
F 4 HOH A 27 1827 27 HOH HOH . 
F 4 HOH A 28 1828 28 HOH HOH . 
F 4 HOH A 29 1829 29 HOH HOH . 
F 4 HOH A 30 1830 30 HOH HOH . 
F 4 HOH A 31 1831 31 HOH HOH . 
F 4 HOH A 32 1832 32 HOH HOH . 
F 4 HOH A 33 1833 33 HOH HOH . 
F 4 HOH A 34 1834 34 HOH HOH . 
F 4 HOH A 35 1835 35 HOH HOH . 
F 4 HOH A 36 1836 36 HOH HOH . 
F 4 HOH A 37 1837 37 HOH HOH . 
F 4 HOH A 38 1838 38 HOH HOH . 
F 4 HOH A 39 1839 39 HOH HOH . 
F 4 HOH A 40 1840 40 HOH HOH . 
F 4 HOH A 41 1841 41 HOH HOH . 
F 4 HOH A 42 1842 42 HOH HOH . 
F 4 HOH A 43 1843 43 HOH HOH . 
F 4 HOH A 44 1844 44 HOH HOH . 
F 4 HOH A 45 1845 45 HOH HOH . 
F 4 HOH A 46 1846 46 HOH HOH . 
F 4 HOH A 47 1847 47 HOH HOH . 
F 4 HOH A 48 1848 48 HOH HOH . 
F 4 HOH A 49 1849 49 HOH HOH . 
F 4 HOH A 50 1850 50 HOH HOH . 
F 4 HOH A 51 1851 51 HOH HOH . 
F 4 HOH A 52 1852 52 HOH HOH . 
F 4 HOH A 53 1853 53 HOH HOH . 
F 4 HOH A 54 1854 54 HOH HOH . 
F 4 HOH A 55 1855 55 HOH HOH . 
F 4 HOH A 56 1856 56 HOH HOH . 
F 4 HOH A 57 1857 57 HOH HOH . 
F 4 HOH A 58 1858 58 HOH HOH . 
F 4 HOH A 59 1859 59 HOH HOH . 
F 4 HOH A 60 1860 60 HOH HOH . 
F 4 HOH A 61 1861 61 HOH HOH . 
F 4 HOH A 62 1862 62 HOH HOH . 
F 4 HOH A 63 1863 63 HOH HOH . 
F 4 HOH A 64 1864 64 HOH HOH . 
F 4 HOH A 65 1865 65 HOH HOH . 
F 4 HOH A 66 1866 66 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 N N6 SOP . . . B 2 21.841 -7.76 -2.622 1 34.23 ? N6 SOP 1701 A 1 
HETATM 2 C C6 SOP . . . B 2 23.136 -8.439 -2.676 1 31.91 ? C6 SOP 1701 A 1 
HETATM 3 N N1 SOP . . . B 2 24.244 -7.789 -3.042 1 32.42 ? N1 SOP 1701 A 1 
HETATM 4 C C2 SOP . . . B 2 25.44 -8.39 -3.104 1 31.34 ? C2 SOP 1701 A 1 
HETATM 5 N N3 SOP . . . B 2 25.61 -9.674 -2.809 1 34.07 ? N3 SOP 1701 A 1 
HETATM 6 C C4 SOP . . . B 2 24.54 -10.418 -2.426 1 36.61 ? C4 SOP 1701 A 1 
HETATM 7 C C5 SOP . . . B 2 23.254 -9.84 -2.338 1 35.44 ? C5 SOP 1701 A 1 
HETATM 8 N N7 SOP . . . B 2 22.385 -10.831 -1.934 1 33.73 ? N7 SOP 1701 A 1 
HETATM 9 C C8 SOP . . . B 2 23.085 -11.961 -1.774 1 33.49 ? C8 SOP 1701 A 1 
HETATM 10 N N9 SOP . . . B 2 24.38 -11.738 -2.066 1 35.35 ? N9 SOP 1701 A 1 
HETATM 11 C C1' SOP . . . B 2 25.325 -12.629 -1.994 1 33.66 ? C1' SOP 1701 A 1 
HETATM 12 O O4' SOP . . . B 2 24.911 -13.901 -2.677 1 30.03 ? O4' SOP 1701 A 1 
HETATM 13 C C2' SOP . . . B 2 25.483 -13.069 -0.492 1 32.49 ? C2' SOP 1701 A 1 
HETATM 14 O O2' SOP . . . B 2 26.398 -12.127 0.219 1 33 ? O2' SOP 1701 A 1 
HETATM 15 C C3' SOP . . . B 2 25.945 -14.225 -0.565 1 30.72 ? C3' SOP 1701 A 1 
HETATM 16 O O3' SOP . . . B 2 27.456 -14.216 -0.61 1 33.76 ? O3' SOP 1701 A 1 
HETATM 17 P P3 SOP . . . B 2 28.298 -15.359 0.081 1 43.69 ? P3 SOP 1701 A 1 
HETATM 18 O O32 SOP . . . B 2 28.197 -16.613 -0.742 1 24.53 ? O32 SOP 1701 A 1 
HETATM 19 O O33 SOP . . . B 2 29.737 -14.8 0.151 1 45.43 ? O33 SOP 1701 A 1 
HETATM 20 O O31 SOP . . . B 2 27.837 -15.602 1.548 1 33.36 ? O31 SOP 1701 A 1 
HETATM 21 C C4' SOP . . . B 2 25.447 -14.854 -2.003 1 27.35 ? C4' SOP 1701 A 1 
HETATM 22 C C5' SOP . . . B 2 24.459 -15.957 -1.812 1 23.09 ? C5' SOP 1701 A 1 
HETATM 23 O O5' SOP . . . B 2 23.297 -15.342 -1.223 1 23.83 ? O5' SOP 1701 A 1 
HETATM 24 P P1 SOP . . . B 2 21.892 -15.547 -1.882 1 26.33 ? P1 SOP 1701 A 1 
HETATM 25 O O11 SOP . . . B 2 21.947 -15.09 -3.313 1 27.02 ? O11 SOP 1701 A 1 
HETATM 26 O O12 SOP . . . B 2 20.88 -14.792 -1.069 1 24.46 ? O12 SOP 1701 A 1 
HETATM 27 O O6 SOP . . . B 2 21.473 -17.113 -1.962 1 27.2 ? O6 SOP 1701 A 1 
HETATM 28 P P2 SOP . . . B 2 21.335 -18.07 -0.698 1 24.46 ? P2 SOP 1701 A 1 
HETATM 29 O O21 SOP . . . B 2 22.403 -17.729 0.347 1 20.22 ? O21 SOP 1701 A 1 
HETATM 30 O O22 SOP . . . B 2 21.409 -19.491 -1.145 1 22.33 ? O22 SOP 1701 A 1 
HETATM 31 O O7 SOP . . . B 2 19.906 -17.774 -0.131 1 26.66 ? O7 SOP 1701 A 1 
HETATM 32 C CP9 SOP . . . B 2 18.95 -17.339 -1.098 1 23.23 ? CP9 SOP 1701 A 1 
HETATM 33 C CP8 SOP . . . B 2 17.61 -17.08 -0.419 1 21.18 ? CP8 SOP 1701 A 1 
HETATM 34 C CPB SOP . . . B 2 16.59 -16.772 -1.535 1 18.43 ? CPB SOP 1701 A 1 
HETATM 35 C CPA SOP . . . B 2 17.118 -18.292 0.433 1 19.64 ? CPA SOP 1701 A 1 
HETATM 36 C CP7 SOP . . . B 2 17.863 -15.89 0.451 1 21.9 ? CP7 SOP 1701 A 1 
HETATM 37 O OP3 SOP . . . B 2 18.355 -14.853 -0.388 1 19.51 ? OP3 SOP 1701 A 1 
HETATM 38 C CP6 SOP . . . B 2 16.649 -15.397 1.214 1 24.05 ? CP6 SOP 1701 A 1 
HETATM 39 O OP2 SOP . . . B 2 16.189 -16.035 2.132 1 21.16 ? OP2 SOP 1701 A 1 
HETATM 40 N NP2 SOP . . . B 2 16.106 -14.127 0.817 1 23.62 ? NP2 SOP 1701 A 1 
HETATM 41 C CP5 SOP . . . B 2 14.959 -13.524 1.49 1 23.4 ? CP5 SOP 1701 A 1 
HETATM 42 C CP4 SOP . . . B 2 13.716 -14.195 1.045 1 26.12 ? CP4 SOP 1701 A 1 
HETATM 43 C CP3 SOP . . . B 2 13.537 -13.954 -0.492 1 31.74 ? CP3 SOP 1701 A 1 
HETATM 44 O OP1 SOP . . . B 2 14.065 -13.02 -1.018 1 28.1 ? OP1 SOP 1701 A 1 
HETATM 45 N NP1 SOP . . . B 2 12.733 -14.868 -1.246 1 23.96 ? NP1 SOP 1701 A 1 
HETATM 46 C CP2 SOP . . . B 2 12.56 -14.636 -2.646 1 27.62 ? CP2 SOP 1701 A 1 
HETATM 47 C CP1 SOP . . . B 2 12.36 -15.996 -3.321 1 32.81 ? CP1 SOP 1701 A 1 
HETATM 48 S S SOP . . . B 2 11.046 -15.814 -4.469 1 31.9 ? S SOP 1701 A 1 
HETATM 49 C CA1 SOP . . . B 2 9.71 -16.772 -3.869 1 31.93 ? CA1 SOP 1701 A 1 
HETATM 50 C CA2 SOP . . . B 2 8.964 -15.819 -2.915 1 35.65 ? CA2 SOP 1701 A 1 
HETATM 51 O OA1 SOP . . . B 2 9.024 -15.969 -1.75 1 32.01 ? OA1 SOP 1701 A 1 
HETATM 52 C CA3 SOP . . . B 2 8.178 -14.642 -3.526 1 37.09 ? CA3 SOP 1701 A 1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    5 
_model_server_stats.query_time_ms           328 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           52 
#