SMTL ID : 7mey.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-mer

Ligands

7 x ZN: ZINC ION(Non-covalent)

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

1 x Z3V: 2-(ethylamino)ethane-1-thiol(Covalent)

Z3V.8: 6 residues within 4Å: Chain B: C.48 Chain C: Y.82, C.88, S.120, P.121 Chain D: G.75 No protein-ligand interaction detected (PLIP)

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

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

D
D

E
F

E3 ubiquitin-protein ligase UBR1

Ubiquitin

Ubiquitin-conjugating enzyme E2 2

Ubiquitin

Monoubiquitinated N-degron

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