4YIK: Crystal structure of human cytosolic 5'(3')-deoxyribonucleotidase in complex with the inhibitor PB-PVU

PDB ID: 4YIKDownload
MMDB ID: 132424
PDB Deposition Date: 2015/3/2
Updated in MMDB: 2017/09
Experimental Method:
x-ray diffraction
Resolution: 1.483  Å
Source Organism:
Similar Structures:
Biological Unit for 4YIK: dimeric; determined by author and by software (PISA)
Molecular Components in 4YIK
Label Count Molecule
Proteins (2 molecules)
2
5'(3')-deoxyribonucleotidase, Mitochondrial
(Gene symbol: NT5M)
Molecule annotation
Chemicals and Non-standard biopolymers (26 molecules)
1
2
MAGNESIUM IONMAGNESIUM ION
2
8
GLYCEROLGLYCEROL
3
2
1-{2-deoxy-3,5-O-[phenyl(phosphono)methylidene]-beta-D-threo-pentofuranosyl}-5-[(E)-2-phosphonoethenyl]pyrimidine-2,4(1H,3H)-dione1-{2-deoxy-3,5-O-[phenyl(phosphono)methylidene]-beta-D-threo-pentofuranosyl}-5-[(E)-2-phosphonoethenyl]pyrimidine-2,4(1H,3H)-dione
4
2
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
5
10
DI(HYDROXYETHYL)ETHERDI(HYDROXYETHYL)ETHER
6
2
PHOSPHATE IONPHOSPHATE ION
* Click molecule labels to explore molecular sequence information.
Citing MMDB
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303