SMTL ID : 7m3q.1

Structure of the Smurf2 HECT Domain with a High Affinity Ubiquitin Variant (UbV)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

Ligands

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: G.30, H.31, R.33 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.31, A:R.33 SO4.2: 2 residues within 4Å: Chain A: R.306, R.309 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.306, A:R.309

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 5 residues within 4Å: Chain A: E.35, K.64, F.65, R.66, G.67 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.35, A:F.65, A:G.67 NA.4: 1 residues within 4Å: Chain A: F.134 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.22

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 3 residues within 4Å: Chain A: Y.138, P.321, Q.323 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: Q.26, L.61, H.135 Ligand excluded by PLIP CL.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.8: 1 residues within 4Å: Chain A: G.70 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: A.344, C.345, N.348 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain A: N.290 Ligand excluded by PLIP

1 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Covalent)

DTT.11: 4 residues within 4Å: Chain A: H.353, T.354, C.355, F.356 No protein-ligand interaction detected (PLIP)

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

EDO.12: 1 residues within 4Å: Chain A: Y.92 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chowdhury, A. et al., Structure of the Smurf2 HECT Domain with a High Affinity Ubiquitin Variant (UbV). To be published

Release Date

2021-04-21

Peptides

E3 ubiquitin-protein ligase SMURF2: A
Ubiquitin variant: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

E3 ubiquitin-protein ligase SMURF2

Ubiquitin variant