SMTL ID : 5ojj.2 (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: 8 residues within 4Å: Chain A: R.84, I.85, C.86, K.91, L.124 Chain B: P.73, H.150 Ligands: ZN.2 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:P.73, A:R.84 Water bridges: B:H.150, A:L.87, A:K.91 Salt bridges: B:H.150, A:K.91 ACT.4: 7 residues within 4Å: Chain B: I.85, C.86, K.91, L.124 Chain C: P.73, H.150 Ligands: ZN.5 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Water bridges: B:L.87, C:H.150 Salt bridges: B:K.91, C:H.150 Hydrophobic interactions: C:P.73 ACT.6: 7 residues within 4Å: Chain A: P.73, H.150 Chain C: R.84, I.85, C.86, K.91 Ligands: ZN.7 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:P.73, C:R.84 Salt bridges: A:H.150, C:K.91 Water bridges: C:L.87

4 x ZN: ZINC ION(Non-covalent)

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

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
D

B
E

C
F

Ubiquitin-conjugating enzyme E2 T

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