SMTL ID : 8ei7.1 (1 other biounit)

Crystal structure of the WWP2 HECT domain in complex with H304, a Helicon Polypeptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.22 Å

Oligo State

hetero-1-1-mer

Ligands

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: Y.98, C.99, T.138, T.310, G.311, T.312 Ligands: ZN.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.98, A:C.99, A:T.310 Water bridges: A:T.312, A:T.312 GOL.2: 5 residues within 4Å: Chain A: M.86, C.88, I.108, N.109, P.110 No protein-ligand interaction detected (PLIP)

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

EDO.3: 3 residues within 4Å: Chain A: L.113, T.114, R.117 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.114 EDO.4: 6 residues within 4Å: Chain A: P.2, D.3, R.4, K.9, E.255, E.373 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.3, A:R.4, A:E.373 Water bridges: A:F.6 EDO.5: 1 residues within 4Å: Chain A: E.180 No protein-ligand interaction detected (PLIP) EDO.6: 2 residues within 4Å: Chain A: L.236, D.237 No protein-ligand interaction detected (PLIP) EDO.7: 3 residues within 4Å: Chain A: H.25, D.50, R.53 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.24, A:S.24, A:D.50 EDO.8: 2 residues within 4Å: Chain A: N.20, R.52 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.20, A:R.52, A:R.52

1 x ZN: ZINC ION(Non-covalent)

ZN.9: 6 residues within 4Å: Chain A: Y.98, T.310, I.324, T.348, N.351 Ligands: GOL.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:Y.98, A:T.310, A:T.348

1 x WHL: N,N'-(1,4-phenylene)diacetamide(Covalent)

WHL.10: 4 residues within 4Å: Chain A: E.265 Chain B: C.8, A.11, C.15 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.11 Hydrogen bonds: B:A.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tokareva, O.S. et al., Recognition and reprogramming of E3 ubiquitin ligase surfaces by alpha-helical peptides. Nat Commun (2023)

Release Date

2023-10-25

Peptides

NEDD4-like E3 ubiquitin-protein ligase WWP2: A
H304: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

NEDD4-like E3 ubiquitin-protein ligase WWP2

H304

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