SMTL ID : 7ojx.1

E2 UBE2K covalently linked to donor Ub, acceptor di-Ub, and RING E3 primed for K48-linked Ub chain synthesis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

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

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.27, C.30, H.50, C.53 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.27, A:C.30, A:H.50, A:C.53 ZN.2: 4 residues within 4Å: Chain A: C.45, H.47, C.64, C.67 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.45, A:H.47, A:C.64, A:C.67

1 x ME7: 1,1'-ethane-1,2-diylbis(1H-pyrrole-2,5-dione)(Covalent)

ME7.3: 4 residues within 4Å: Chain B: D.125, C.126 Chain C: R.77 Chain D: C.48 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nakasone, M.A. et al., Structure of UBE2K-Ub/E3/polyUb reveals mechanisms of K48-linked Ub chain extension. Nat.Chem.Biol. (2022)

Release Date

2022-01-12

Peptides

E3 ubiquitin-protein ligase RNF38: A
Ubiquitin-conjugating enzyme E2 K: B
Polyubiquitin-B: C
Polyubiquitin-B: D
Polyubiquitin-B: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

E3 ubiquitin-protein ligase RNF38

Ubiquitin-conjugating enzyme E2 K

Polyubiquitin-B

Polyubiquitin-B

Polyubiquitin-B

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