SMTL ID : 7mex.1

Structure of yeast Ubr1 in complex with Ubc2 and N-degron

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

7 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain D: C.136, C.139, H.157, H.160 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.136, D:C.139, D:H.157, D:H.160 ZN.2: 4 residues within 4Å: Chain D: C.123, C.148, C.151, C.175 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.123, D:C.148, D:C.151, D:C.175 ZN.3: 4 residues within 4Å: Chain D: H.118, C.151, C.177, C.189 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.118, D:C.151, D:C.177, D:C.189 ZN.4: 4 residues within 4Å: Chain D: C.1703, C.1706, H.1722, C.1727 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.1703, D:C.1706, D:H.1722, D:C.1727 ZN.5: 4 residues within 4Å: Chain D: C.1295, H.1297, C.1320, C.1323 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.1295, D:H.1297, D:C.1320, D:C.1323 ZN.6: 4 residues within 4Å: Chain D: C.1220, C.1223, H.1300, C.1303 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.1220, D:C.1223, D:H.1300, D:C.1303 ZN.7: 5 residues within 4Å: Chain D: H.161, Y.933, D.952, H.1763, D.1775 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:H.161, D:D.952, D:H.1763, D:D.1775, D:D.1775

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pan, M. et al., Structural insights into Ubr1-mediated N-degron polyubiquitination. Nature (2021)

Release Date

2021-11-24

Peptides

Ubiquitin: A
Ubiquitin-conjugating enzyme E2 2: B
N-degron: C
E3 ubiquitin-protein ligase UBR1: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
B

C
D

D
A

Ubiquitin

Ubiquitin-conjugating enzyme E2 2

N-degron

E3 ubiquitin-protein ligase UBR1

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