SMTL ID : 6nyd.1

Crystal Structure of S. cerevisiae Ubc3 (Cdc34)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: Y.91, C.97, H.102 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.97, A:H.102 ZN.2: 3 residues within 4Å: Chain A: D.146, D.150, Q.157 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.146, H2O.1 ZN.3: 2 residues within 4Å: Chain A: H.32, E.34 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.32, A:E.34, H2O.4, H2O.4 ZN.4: 2 residues within 4Å: Chain A: E.53, H.58 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.53, A:E.53, A:H.58, H2O.4

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

ACT.5: 3 residues within 4Å: Chain A: I.128, S.129, S.132 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.129 ACT.6: 6 residues within 4Å: Chain A: F.74, S.75, P.76, Q.103, S.104, W.117 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.103 Hydrogen bonds: A:F.74 ACT.7: 4 residues within 4Å: Chain A: S.39, N.40, I.41, F.42 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:I.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Williams, K.M. et al., Structural insights into E1 recognition and the ubiquitin-conjugating activity of the E2 enzyme Cdc34. Nat Commun (2019)

Release Date

2019-08-07

Peptides

Ubiquitin-conjugating enzyme E2-34 kDa: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Ubiquitin-conjugating enzyme E2-34 kDa

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