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Crystal structure of human NUDT5 complexed with 8-oxo-dgmp

Analyse Crystal structure of human NUDT5 complexed with 8-oxo-dgmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3L85
Type: protein
Length: 390 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ADP-sugar pyrophosphatase
EC: 3.6.1.13
UniProt: Q9UKK9
Ligands: 8OG
Pockets: 2 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 24% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	ADP-sugar pyrophosphatase (EC 3.6.1.13)	protein	195	24% helix, 43% strand	Q9UKK9

Ligands and binding sites

8OG · 8-oxo-2'-deoxy-guanosine-5'-monophosphate · ligand · 2 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	421	0.72	0.83	40	8OG
2	384	0.71	0.82	42	8OG

Interfaces

1 interface between chains.

A–B · 3132 Å² buried · 22 hydrogen bonds · protein-protein

Compared structures

3L85 · Crystal structure of human NUDT5 complexed with 8-oxo-dGMP · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9UKK9
Elsewhere: RCSB PDB 3L85 · PDBe 3L85 · UniProt Q9UKK9

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