SMTL ID : 6nyo.1

Crystal structure of a human Cdc34-ubiquitin thioester mimetic

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-1-1-mer

Ligands

1 x U94: 4,5-dideoxy-5-(3',5'-dichlorobiphenyl-4-yl)-4-[(methoxyacetyl)amino]-L-arabinonic acid(Non-covalent)

U94.1: 18 residues within 4Å: Chain A: F.30, I.47, F.48, P.50, N.52, T.53, L.54, Y.55, F.60, I.130, L.133, N.134, W.153, Y.192 Chain B: G.67, K.68, E.71, R.74 14 PLIP interactions: 8 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:I.47, A:P.50, A:T.53, A:Y.55, A:Y.55, A:L.133, A:L.133 Hydrogen bonds: A:L.54, B:K.68 Water bridges: B:Q.69, B:E.71, B:E.71 Salt bridges: B:K.68, B:R.74

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 4 residues within 4Å: Chain A: K.65, F.66, P.67, P.74 1 PLIP interactions: 1 interactions with chain A Water bridges: A:P.74 EDO.4: 4 residues within 4Å: Chain B: T.27, L.28, T.29, L.89 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.28, B:T.29, B:L.89 EDO.5: 5 residues within 4Å: Chain A: E.135, P.136, N.137 Chain B: R.92, L.93 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.92, B:R.92, A:P.136 Water bridges: A:E.135, A:T.138

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 4 residues within 4Å: Chain A: Y.41, F.66, P.67, I.68 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.66 Water bridges: A:I.68

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 R2: A
Ubiquitin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

Ubiquitin-conjugating enzyme E2 R2

Ubiquitin

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