SMTL ID : 5tdc.1 (1 other biounit)

Crystal structure of the human UBR-box domain from UBR1 in complex with monomethylated arginine peptide.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

monomer

Ligands

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

NMM-ILE-PHE.1: 14 residues within 4Å: Chain A: D.26, P.27, T.28, C.29, V.30, H.49, G.55, F.56, C.57, D.58, D.61, E.63, A.64 Ligands: SO4.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.30 Hydrogen bonds: A:T.28, A:T.28, A:F.56, A:F.56 Salt bridges: A:D.58, A:D.61

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 7 residues within 4Å: Chain A: C.7, R.9, C.32, C.35, C.57, C.59, H.74 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.7, A:C.32, A:C.35, A:C.57 ZN.3: 6 residues within 4Å: Chain A: C.7, C.35, C.59, C.71, N.73, 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, V.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 SO4: SULFATE ION(Non-functional Binders)

SO4.5: 9 residues within 4Å: Chain A: F.11, H.49, S.51, T.52, G.53, G.54, G.55 Ligands: NMM-ILE-PHE.1, NMM-ILE-PHE.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.51, A:T.52, A:T.52, A:T.52, A:G.53, A:G.55 Water bridges: A:H.49 Salt bridges: A:H.49

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 UBR1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E3 ubiquitin-protein ligase UBR1

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