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Crystal structure of POLY(ADP-ribose) glycohydrolase (parg) from deinococcus radiodurans in complex with ADP-ribose (P32)

Analyse Crystal structure of POLY(ADP-ribose) glycohydrolase (parg) from deinococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ZDC
Type: protein
Length: 1,502 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Poly ADP-ribose glycohydrolase
UniProt: Q9RZM4
Ligands: AR6, PO4
Pockets: 20 · best druggability 0.74

Structure

x-ray diffraction · 5 distinct chains · 46% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Poly ADP-ribose glycohydrolase	protein	253	45% helix, 19% strand	Q9RZM4
F	Poly ADP-ribose glycohydrolase	protein	252	46% helix, 19% strand	Q9RZM4
H, J	Poly ADP-ribose glycohydrolase	protein	250	46% helix, 19% strand	Q9RZM4
L	Poly ADP-ribose glycohydrolase	protein	248	46% helix, 19% strand	Q9RZM4
D	Poly ADP-ribose glycohydrolase	protein	249	46% helix, 19% strand	Q9RZM4

Ligands and binding sites

AR6 · [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2R,3S,4R,5S)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate · ligand · 6 copies · chains C, F, H, J, L, D
PO4 · Phosphate ion · ion · 3 copies · chains C, J, F, L, H, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	638	0.74	0.81	82	AR6
2	432	0.69	0.81	63	AR6
3	327	0.69	0.82	45	AR6
4	355	0.68	0.81	51	AR6
5	286	0.67	0.83	46	AR6

Interfaces

5 interfaces between chains.

F–L · 1036 Å² buried · 27 hydrogen bonds · protein-protein
C–J · 1020 Å² buried · 21 hydrogen bonds · protein-protein
H–D · 1015 Å² buried · 24 hydrogen bonds · protein-protein
C–H · 635 Å² buried · 7 hydrogen bonds · protein-protein
F–H · 531 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5ZDC · Crystal structure of poly(ADP-ribose) glycohydrolase (PARG) from Deinococcus radiodurans… · the same entry in another collection · chain C against C, TM-score 1.00

Analyse

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Every structure of UniProt Q9RZM4
Elsewhere: RCSB PDB 5ZDC · PDBe 5ZDC · UniProt Q9RZM4

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