SMTL ID : 8z30.1

Crystal structure of HOIP PUB domain in complex with tolfenamic acid complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

3 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 5 residues within 4Å: Chain A: R.55, A.58, L.174, L.175 Ligands: TLF.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.55 PEG.4: 4 residues within 4Å: Chain B: V.54, R.55, L.174 Ligands: TLF.5 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.55 PEG.7: 8 residues within 4Å: Chain A: N.98, P.100, R.103 Chain B: H.59 Chain C: V.54, R.55, L.174 Ligands: TLF.8 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.55

3 x TLF: 2-[(3-chloro-2-methylphenyl)amino]benzoic acid(Non-covalent)

TLF.2: 9 residues within 4Å: Chain A: L.41, A.51, E.156, L.157, L.160, L.171, L.174, L.175 Ligands: PEG.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.41, A:L.41, A:A.51, A:L.157, A:L.160, A:L.175 Water bridges: A:L.41, A:R.44 TLF.5: 8 residues within 4Å: Chain B: L.41, R.44, A.51, E.156, L.157, L.160, L.175 Ligands: PEG.4 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.41, B:L.41, B:A.51, B:L.157, B:L.160, B:L.175 Water bridges: B:R.44 TLF.8: 11 residues within 4Å: Chain A: N.98 Chain C: L.41, R.44, A.51, E.156, L.157, L.160, L.171, L.174, L.175 Ligands: PEG.7 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.41, C:L.41, C:L.160, C:L.174, C:L.175 Water bridges: C:R.44 Hydrogen bonds: A:N.98

1 x PE4: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-functional Binders)

PE4.3: 10 residues within 4Å: Chain A: R.103, D.107, V.109, Q.110, R.113 Chain B: R.103, D.107, V.109, Q.110, R.113 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Q.110 Hydrogen bonds: B:R.103, A:R.103, A:R.113

1 x TOE: 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL(Non-covalent)

TOE.6: 4 residues within 4Å: Chain B: R.55 Chain C: D.107, Q.110, R.113 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Water bridges: C:G.112, C:G.112 Hydrogen bonds: B:R.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhong, F. et al., Repurposing Tolfenamic Acid to Anchor the Uncharacterized Pocket of the PUB Domain for Proteolysis of the Atypical E3 Ligase HOIP. Acs Chem.Biol. (2024)

Release Date

2024-11-27

Peptides

E3 ubiquitin-protein ligase RNF31: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

E3 ubiquitin-protein ligase RNF31

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