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Crystal structure of human JMJD5 jmj-C domain

Analyse Crystal structure of human JMJD5 jmj-C domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4QU1
Type: protein
Length: 236 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysine-specific demethylase 8
EC: 1.14.11.27
UniProt: Q8N371
Ligands: AKG, NI
Pockets: 1 · best druggability 0.54

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysine-specific demethylase 8 (EC 1.14.11.27)	protein	236	25% helix, 33% strand	Q8N371

Ligands and binding sites

AKG · 2-oxoglutaric acid · ligand · chains A
NI · Nickel (II) ion · metal · chains A
GOL · Glycerol · 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	121	0.54	0.82	25	NI, AKG

Compared structures

4QU1 · Crystal structure of human JMJD5 jmj-c domain · the same entry in another collection · chain A against A, TM-score 1.00
Q8N371 · AlphaFold monomer V2.0 prediction for bifunctional peptidase and arginyl-hydroxylase… · a predicted model of the same protein · chain A against A, TM-score 1.00

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 Q8N371
Elsewhere: RCSB PDB 4QU1 · PDBe 4QU1 · UniProt Q8N371

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