MolNFT v1 · #119821 · protein

Crystal structure of mycobacterium smegmatis MUTT1 in complex with 8- oxo-dgdp

5GGB · Hydrolase, nudix family protein: “Crystal structure of mycobacterium smegmatis MUTT1 in complex with 8- oxo-dgdp”. X-ray diffraction, 1 ligand (8GD), 3 pockets (best druggability 0.49). MolNFT v1 #119821 on GenesisL1: 3D structure…

PDB: 5GGB
Type: protein
Length: 290 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hydrolase, nudix family protein
UniProt: A0QUZ2
Ligands: 8GD
Pockets: 3 · best druggability 0.49

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 34% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hydrolase, nudix family protein	protein	290	35% helix, 34% strand	A0QUZ2

Ligands and binding sites

8GD · 2'-deoxy-8-oxoguanosine 5'-(trihydrogen diphosphate) · ligand · chains A

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	83	0.49	0.83	20	empty
2	66	0.44	0.82	16	empty
3	112	0.41	0.76	19	empty

Compared structures

5GGB · Crystal structure of Mycobacterium smegmatis MutT1 in complex with 8-oxo-dGDP · the same entry in another collection · chain A against A, TM-score 1.00
A0QUZ2 · AlphaFold monomer V2.0 prediction for 8-oxo-(D)GTP phosphatase (A0QUZ2) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 A0QUZ2
Elsewhere: RCSB PDB 5GGB · PDBe 5GGB · UniProt A0QUZ2

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