MolNFT v1 · #62309 · protein

Crystal structure of human PPPDE1

3EBQ · Molecule: PPPDE1 (permuted papain fold peptidases of dsrna…: “Crystal structure of human PPPDE1”. X-ray diffraction, 1 ligand (HG), 1 pocket (best druggability 0.56). MolNFT v1 #62309 on GenesisL1: 3D structure, binding sites and…

PDB: 3EBQ
Type: protein
Length: 144 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Molecule: PPPDE1 (permuted papain fold peptidases of dsrna viruses and eukaryotes 1)…
EC: 3.4.22.-
UniProt: Q6ICB0
Ligands: HG
Pockets: 1 · best druggability 0.56

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Molecule: PPPDE1 (permuted papain fold peptidases of dsrna viruses and eukaryotes 1), UPF0326 protein FAM152B (EC 3.4.22.-)	protein	144	38% helix, 23% strand	Q6ICB0

Ligands and binding sites

HG · Mercury (II) ion · metal · 2 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	226	0.56	0.78	32	HG

Compared structures

3EBQ · Crystal structure of human PPPDE1 · the same entry in another collection · chain A against A, TM-score 1.00
Q6ICB0 · AlphaFold monomer V2.0 prediction for desumoylating isopeptidase 1 (Q6ICB0) · a predicted model of the same protein · chain A against A, TM-score 0.98

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q6ICB0
Elsewhere: RCSB PDB 3EBQ · PDBe 3EBQ · UniProt Q6ICB0

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