SMTL ID : 6jlq.1

Crystal structure of human USP46-WDR48-WDR20 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.10 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.160, C.163, C.207, T.209, C.210 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.160, A:C.163, A:C.207, A:C.210

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 1 residues within 4Å: Chain A: K.234 No protein-ligand interaction detected (PLIP) GOL.4: 4 residues within 4Å: Chain B: S.278, G.280, Q.281, I.285 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.278, B:Q.281, B:Q.281 GOL.5: 3 residues within 4Å: Chain B: M.150, S.151, T.152 No protein-ligand interaction detected (PLIP) GOL.6: 2 residues within 4Å: Chain B: K.128, H.145 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.145 GOL.7: 6 residues within 4Å: Chain B: N.301, H.306, Y.308, P.349, I.369, H.370 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.301 GOL.8: 6 residues within 4Å: Chain B: R.179, Q.180, L.204, S.205, G.206, N.207 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.206, B:N.207 GOL.9: 1 residues within 4Å: Chain B: R.314 No protein-ligand interaction detected (PLIP) GOL.10: 3 residues within 4Å: Chain C: D.71, L.417, D.419 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.419, C:D.419

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

PO4.3: 3 residues within 4Å: Chain B: R.233, K.242, K.245 4 PLIP interactions: 4 interactions with chain B Salt bridges: B:K.208, B:R.233, B:K.242, B:K.245

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhu, H. et al., Structural insights into the activation of USP46 by WDR48 and WDR20. Cell Discov (2019)

Release Date

2019-07-10

Peptides

Ubiquitin carboxyl-terminal hydrolase 46: A
WD repeat-containing protein 48: B
WD repeat-containing protein 20,highly similar to WD repeat protein 20,WD repeat-containing protein 20: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Ubiquitin carboxyl-terminal hydrolase 46

WD repeat-containing protein 48

WD repeat-containing protein 20,highly similar to WD repeat protein 20,WD repeat-containing protein 20