SMTL ID : 8ei5.1 (3 other biounits)

Crystal structure of the WWP2 HECT domain in complex with H301, a Helicon Polypeptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: Y.98, T.310, I.324, T.348, N.351 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.310, A:T.348

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: M.86, C.88, I.108, N.109, P.110 Ligands: EDO.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.109 GOL.3: 5 residues within 4Å: Chain A: C.99, T.138, L.139, P.140, G.311 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.99, A:L.139 Water bridges: A:L.100 GOL.4: 7 residues within 4Å: Chain A: C.99, L.100, Q.101, T.138, P.140, F.141, F.224 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.138, A:P.140 Water bridges: A:L.100, A:I.102, A:T.138

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

EDO.5: 2 residues within 4Å: Chain A: D.270, G.318 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.270 Water bridges: A:D.267 EDO.6: 3 residues within 4Å: Chain A: E.246, W.247, R.249 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.246, A:R.249, A:R.249 EDO.7: 5 residues within 4Å: Chain A: C.261, G.262, Q.264, C.313, R.314 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.262, A:Q.264 EDO.8: 3 residues within 4Å: Chain A: M.86, Y.87 Ligands: GOL.2 No protein-ligand interaction detected (PLIP) EDO.9: 4 residues within 4Å: Chain A: Q.272, T.275, Y.277, K.282 No protein-ligand interaction detected (PLIP) EDO.10: 4 residues within 4Å: Chain A: Y.280, K.285, Q.286, K.336 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.336, A:K.336 EDO.12: 4 residues within 4Å: Chain A: E.161, N.164, S.165 Chain B: Q.10 No protein-ligand interaction detected (PLIP)

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

WHL.11: 8 residues within 4Å: Chain A: C.177, G.178, L.179, E.180 Chain B: C.8, A.11, A.12, C.15 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.11, B:A.12 Hydrogen bonds: B:C.8, A:E.180

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
H301: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

NEDD4-like E3 ubiquitin-protein ligase WWP2

H301

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