SMTL ID : 5tdb.1

Crystal structure of the human UBR-box domain from UBR2 in complex with asymmetrically double methylated arginine peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.10 Å

Oligo State

monomer

Ligands

1 x DA2- ILE: DA2-ILE-PHE-SER peptide(Non-covalent)

DA2-ILE.1: 17 residues within 4Å: Chain A: F.11, T.17, V.25, D.26, P.27, T.28, C.29, V.30, R.47, T.49, G.54, G.55, F.56, D.58, D.61, E.63, A.64 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.30, A:V.30 Hydrogen bonds: A:T.28, A:F.56, A:D.58 Water bridges: A:D.58 Salt bridges: A:D.26, A:D.58

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: C.7, R.9, C.32, C.35, C.57, C.59 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.7, A:C.32, A:C.35, A:C.57 ZN.3: 5 residues within 4Å: Chain A: C.7, C.35, C.59, C.71, H.74 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.35, A:C.59, A:C.71, A:H.74 ZN.4: 6 residues within 4Å: Chain A: C.20, D.22, C.23, I.40, H.41, H.44 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.20, A:C.23, A:H.41, A:H.44

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

EDO.5: 5 residues within 4Å: Chain A: V.25, T.62, E.63, W.65, K.66 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Munoz-Escobar, J. et al., Bound Waters Mediate Binding of Diverse Substrates to a Ubiquitin Ligase. Structure (2017)

Release Date

2017-03-22

Peptides

E3 ubiquitin-protein ligase UBR2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E3 ubiquitin-protein ligase UBR2

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