SMTL ID : 8oyp.2 (1 other biounit)

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

Coordinates

PDB Format

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: 4 residues within 4Å: Chain A: Q.142, W.149, L.167, W.359 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.142 NO3.4: 5 residues within 4Å: Chain A: Y.422, H.429, Y.444, D.446 Chain B: G.78 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.78

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 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 6 PLIP interactions: 2 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:A.148, A:F.184, B:Q.62, B:Q.62, B:S.65, B:S.65

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

PO4.6: 5 residues within 4Å: Chain A: R.379, R.426 Chain B: Q.40, R.72, R.74 8 PLIP interactions: 2 interactions with chain B, 6 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, A:R.379, A:R.379

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
B

B
D

Ubiquitin carboxyl-terminal hydrolase 11,Response regulator FrzS

Polyubiquitin-B

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