SMTL ID : 2y6e.1

Structure of the D1D2 domain of USP4, the conserved catalytic domain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-hexamer

Ligands

6 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.168, C.171, C.234, C.237 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.168, A:C.171, A:C.234, A:C.237 ZN.3: 4 residues within 4Å: Chain B: C.168, C.171, C.234, C.237 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.168, B:C.171, B:C.234, B:C.237 ZN.4: 4 residues within 4Å: Chain C: C.168, C.171, C.234, C.237 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.168, C:C.171, C:C.234, C:C.237 ZN.6: 4 residues within 4Å: Chain D: C.168, C.171, C.234, C.237 No protein-ligand interaction detected (PLIP) ZN.7: 2 residues within 4Å: Chain E: C.168, C.171 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:C.168 ZN.8: 2 residues within 4Å: Chain F: C.168, C.171 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:C.168, F:C.171

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 7 residues within 4Å: Chain A: Q.98, M.312, G.313 Chain B: A.78, R.80 Chain C: K.55, R.88 10 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B, 6 interactions with chain C Hydrogen bonds: A:Q.98, A:G.313 Water bridges: A:A.311, C:K.55, C:K.55, C:R.88, C:R.88 Salt bridges: B:R.80, C:K.55, C:R.88 SO4.5: 5 residues within 4Å: Chain C: F.162, F.181, Y.183, L.184, T.185 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.185 Water bridges: C:Y.183

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Clerici, M. et al., The Dusp-Ubl Domain of Usp4 Enhances its Catalytic Efficiency by Promoting Ubiquitin Exchange. Nat.Commun. (2014)

Release Date

2011-04-06

Peptides

UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 4: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 4