SMTL ID : 2znr.1

Crystal structure of the DUB domain of human AMSH-LP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.104, C.144, H.150, H.152 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.104, A:C.144, A:H.150, A:H.152 ZN.2: 4 residues within 4Å: Chain A: E.34, H.89, H.91, D.102 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.89, A:H.91, A:D.102, A:D.102, H2O.3

1 x PR: PRASEODYMIUM ION(Non-covalent)

PR.3: 1 residues within 4Å: Chain A: D.169 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.169, H2O.11, H2O.11, H2O.11, H2O.11

7 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 2 residues within 4Å: Chain A: K.171, I.173 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.171 Water bridges: A:K.20, A:K.20, A:I.172 EDO.5: 6 residues within 4Å: Chain A: L.13, P.14, E.15, L.17, C.18, V.167 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.14, A:L.17, A:C.18 Water bridges: A:H.19 EDO.6: 3 residues within 4Å: Chain A: I.130, C.162, V.165 2 PLIP interactions: 2 interactions with chain A Water bridges: A:C.162, A:V.165 EDO.7: 4 residues within 4Å: Chain A: T.49, T.51, I.170, K.171 2 PLIP interactions: 2 interactions with chain A Water bridges: A:K.42, A:K.171 EDO.8: 3 residues within 4Å: Chain A: R.9, L.43, N.46 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.9, A:R.9, A:N.46 Water bridges: A:N.46 EDO.9: 2 residues within 4Å: Chain A: E.47, L.166 No protein-ligand interaction detected (PLIP) EDO.10: 3 residues within 4Å: Chain A: K.57, L.177, R.178 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.57, A:R.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sato, Y. et al., Structural basis for specific cleavage of Lys 63-linked polyubiquitin chains. Nature (2008)

Release Date

2008-09-02

Peptides

AMSH-like protease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

AMSH-like protease