SMTL ID : 8oyp.1 (1 other biounit)

Crystal structure of Ubiquitin specific protease 11 (USP11) in complex with a substrate mimetic

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.44 Å

Oligo State

hetero-1-1-mer

Ligands

1 x CD: CADMIUM ION(Non-covalent)

CD.1: 4 residues within 4Å: Chain A: C.174, C.177, C.343, C.346 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.174, A:C.177, A:C.343, A:C.346

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 3 residues within 4Å: Chain A: K.128, R.155, N.156 Ligand excluded by PLIP

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.3: 3 residues within 4Å: Chain A: G.312, A.313, F.317 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.312 NO3.4: 4 residues within 4Å: Chain A: Q.142, Q.146, W.149, W.359 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.142, A:Q.146, A:W.359

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 5 residues within 4Å: Chain A: R.379, R.426 Chain B: Q.40, R.72, R.74 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Salt bridges: B:R.72, B:R.74, A:R.379, A:R.426 Water bridges: A:R.379, A:R.379

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 10 residues within 4Å: Chain A: L.133, A.148, T.183, F.184, D.185, P.186 Chain B: F.45, N.60, Q.62, S.65 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:Q.62, B:S.65, A:A.148, A:D.185

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maurer, S.K. et al., Ubiquitin-specific protease 11 structure in complex with an engineered substrate mimetic reveals a molecular feature for deubiquitination selectivity. J.Biol.Chem. (2023)

Release Date

2023-10-18

Peptides

Ubiquitin carboxyl-terminal hydrolase 11,Response regulator FrzS: A
Polyubiquitin-B: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Ubiquitin carboxyl-terminal hydrolase 11,Response regulator FrzS

Polyubiquitin-B

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