MolNFT v1 · #123466 · protein

Crystal structure of deubiquitinase mindy-1

5JKN · Protein FAM63A: “Crystal structure of deubiquitinase mindy-1”. X-ray diffraction, 2 ligands (HG, PO4), 1 pocket (best druggability 0.52). MolNFT v1 #123466 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5JKN
Type: protein
Length: 256 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein FAM63A
UniProt: Q8N5J2
Ligands: HG, PO4
Pockets: 1 · best druggability 0.52

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein FAM63A	protein	256	38% helix, 21% strand	Q8N5J2

Ligands and binding sites

HG · Mercury (II) ion · metal · chains A
PO4 · Phosphate ion · ion · chains A
PEG · Di(hydroxyethyl)ether · additive · 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	180	0.52	0.78	27	PO4

Compared structures

5JKN · Crystal structure of deubiquitinase MINDY-1 · the same entry in another collection · chain A against A, TM-score 1.00
Q8N5J2 · AlphaFold monomer V2.0 prediction for ubiquitin carboxyl-terminal hydrolase mindy-1… · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q8N5J2
Elsewhere: RCSB PDB 5JKN · PDBe 5JKN · UniProt Q8N5J2

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