SMTL ID : 4fjv.3 (2 other biounits)

Crystal Structure of Human Otubain2 and Ubiquitin Complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-2-2-mer

Ligands

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 9 residues within 4Å: Chain A: F.9, N.10, L.11, S.13, K.47, T.48, K.49 Chain C: R.23 Ligands: GOL.6 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:K.47, C:R.23 GOL.2: 7 residues within 4Å: Chain A: K.15, D.17 Chain C: K.15, C.16, D.17, T.43, A.44 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:K.15, A:D.17, C:D.17, C:T.43 GOL.3: 7 residues within 4Å: Chain A: Y.198, V.199, D.200, Y.223, K.224, T.225, S.226 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.223, A:T.225, A:S.226, A:S.226 GOL.5: 7 residues within 4Å: Chain A: R.23 Chain C: F.9, N.10, S.13, K.47, T.48 Ligands: GOL.7 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:R.23, C:F.9 Water bridges: C:G.50 GOL.6: 5 residues within 4Å: Chain A: S.13, E.14, C.16 Chain C: R.23 Ligands: GOL.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.13, A:S.13 GOL.7: 6 residues within 4Å: Chain A: R.23 Chain C: S.13, E.14, C.16, K.47 Ligands: GOL.5 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.13, C:S.13, C:E.14 Water bridges: C:K.47

2 x NEH: ETHANAMINE(Covalent)

NEH.4: 6 residues within 4Å: Chain A: G.52, C.54, E.177, S.226, H.227 Chain B: G.85 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.226 NEH.8: 6 residues within 4Å: Chain C: G.52, C.54, E.177, S.226, H.227 Chain D: G.85 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.226

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Altun, M. et al., The human otubain2-ubiquitin structure provides insights into the cleavage specificity of poly-ubiquitin-linkages. Plos One (2015)

Release Date

2013-06-12

Peptides

Ubiquitin thioesterase OTUB2: AC
Polyubiquitin-C: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Ubiquitin thioesterase OTUB2

Polyubiquitin-C

Related Entries With Identical Sequence