SMTL ID : 6nft.2 (1 other biounit)

Structure of USP5 zinc-finger ubiquitin binding domain co-crystallized with (4-oxoquinazolin-3(4H)-yl)acetic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.30, C.33, C.50, H.63 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.30, A:C.33, A:C.50, A:H.63

1 x KKG: (4-oxoquinazolin-3(4H)-yl)acetic acid(Non-covalent)

KKG.2: 10 residues within 4Å: Chain A: W.40, G.51, R.52, Y.54, A.64, V.65, Y.90, Y.92, D.95, M.97 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.90 Hydrogen bonds: A:R.52, A:R.52, A:V.65, A:Y.92, A:Y.92 Water bridges: A:G.60 Salt bridges: A:R.52 pi-Stacking: A:Y.90

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

EDO.3: 5 residues within 4Å: Chain A: L.17, D.18, N.19, P.20, D.45 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.17 Water bridges: A:L.17 EDO.4: 5 residues within 4Å: Chain A: Q.6, V.7, E.94, D.96, V.98 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.7, A:D.96, A:D.96

6 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.5: 3 residues within 4Å: Chain A: D.95, D.96 Ligands: UNX.6 No protein-ligand interaction detected (PLIP) UNX.6: 4 residues within 4Å: Chain A: E.94, D.95, D.96 Ligands: UNX.5 No protein-ligand interaction detected (PLIP) UNX.7: 1 residues within 4Å: Chain A: D.96 No protein-ligand interaction detected (PLIP) UNX.8: 4 residues within 4Å: Chain A: E.37, N.38, L.39, L.79 No protein-ligand interaction detected (PLIP) UNX.9: 5 residues within 4Å: Chain A: I.23, P.24, P.25, G.111, I.112 No protein-ligand interaction detected (PLIP) UNX.10: 2 residues within 4Å: Chain A: L.99, D.100 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mann, M.K. et al., Discovery of Small Molecule Antagonists of the USP5 Zinc Finger Ubiquitin-Binding Domain. J.Med.Chem. (2019)

Release Date

2019-01-02

Peptides

Ubiquitin carboxyl-terminal hydrolase 5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Ubiquitin carboxyl-terminal hydrolase 5

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