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

Crystal structure of the Zn-bound ubiquitin-conjugating enzyme Ube2T

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-trimer

Ligands

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 7 residues within 4Å: Chain A: I.85, C.86, K.91, L.124 Chain C: P.73, H.150 Ligands: ZN.2 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:P.73 Water bridges: C:H.150, A:L.87 Salt bridges: C:H.150, A:K.91 ACT.5: 6 residues within 4Å: Chain A: P.73, H.150 Chain B: I.85, C.86, K.91 Ligands: ZN.6 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.73 Hydrogen bonds: A:H.150 Salt bridges: A:H.150, B:K.91 Water bridges: B:L.87 ACT.7: 7 residues within 4Å: Chain B: P.73, H.150 Chain C: I.85, C.86, K.91, L.124 Ligands: ZN.8 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Water bridges: C:L.87, B:H.150 Salt bridges: C:K.91, B:H.150 Hydrophobic interactions: B:P.73

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: C.86, K.91 Chain C: K.149, H.150 Ligands: ACT.1 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: C:H.150, A:C.86, ACT.1 ZN.4: 3 residues within 4Å: Chain A: D.127 Chain B: D.127 Chain C: D.127 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain C, 1 interactions with chain B Metal complexes: A:D.127, A:D.127, C:D.127, C:D.127, B:D.127 ZN.6: 5 residues within 4Å: Chain A: K.149, H.150 Chain B: C.86, K.91 Ligands: ACT.5 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: B:C.86, A:H.150, ACT.5 ZN.8: 5 residues within 4Å: Chain B: K.149, H.150 Chain C: C.86, K.91 Ligands: ACT.7 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: B:H.150, C:C.86, ACT.7

2 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 3 residues within 4Å: Chain A: N.119, D.122 Chain C: K.149 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.119, A:D.122 Water bridges: A:C.86, A:D.122, A:D.122, A:D.122, A:D.122 TRS.9: 4 residues within 4Å: Chain B: K.149 Chain C: D.88, N.119, D.122 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:D.88, C:N.119, B:K.149, B:K.149

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morreale, F.E. et al., Mind the Metal: A Fragment Library-Derived Zinc Impurity Binds the E2 Ubiquitin-Conjugating Enzyme Ube2T and Induces Structural Rearrangements. J. Med. Chem. (2017)

Release Date

2017-10-04

Peptides

Ubiquitin-conjugating enzyme E2 T: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Ubiquitin-conjugating enzyme E2 T

Related Entries With Identical Sequence