MolNFT v1 · #168859 · protein

Sdea dub domain in complex with ubiquitin

6WTG · UBIQUITINATING/DEUBIQUITINATING enzyme sdea: “Sdea dub domain in complex with ubiquitin”. X-ray diffraction, 2 pockets (best druggability 0.51). MolNFT v1 #168859 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6WTG
Type: protein
Length: 245 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: UBIQUITINATING/DEUBIQUITINATING enzyme sdea; Ubiquitin
EC: 3.4.22.-, 2.3.2.-, 2.4.2.31
UniProt: Q5ZTK4, P0CG48
Pockets: 2 · best druggability 0.51

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	UBIQUITINATING/DEUBIQUITINATING enzyme sdea (EC 3.4.22.-, 2.3.2.-, 2.4.2.31)	protein	169	45% helix, 22% strand	Q5ZTK4
D	Ubiquitin	protein	76	25% helix, 37% strand	P0CG48

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	79	0.51	0.84	16	empty
2	57	0.25	0.72	12	empty

Interfaces

1 interface between chains.

A–D · 875 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

6WTG · SdeA DUB Domain in complex with Ubiquitin · the same entry in another collection · chain A against A, TM-score 1.00
Q5ZTK4 · AlphaFold monomer V2.0 prediction for UBIQUITINATING/DEUBIQUITINATING enzyme sdea (Q5ZTK4) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 Q5ZTK4
Every structure of UniProt P0CG48
Elsewhere: RCSB PDB 6WTG · PDBe 6WTG · UniProt Q5ZTK4 · UniProt P0CG48

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