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Dpy-21 in complex with FE(II) and alpha-ketoglutarate

Analyse Dpy-21 in complex with FE(II) and alpha-ketoglutarate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5UQD
Type: protein
Length: 324 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dumpy: shorter than wild-type
UniProt: Q9GRZ3
Ligands: AKG, FE2
Pockets: 3 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain · 29% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dumpy: shorter than wild-type	protein	324	29% helix, 31% strand	Q9GRZ3

Ligands and binding sites

AKG · 2-oxoglutaric acid · ligand · chains A
FE2 · Fe (II) ion · metal · chains A
PG0 · 2-(2-methoxyethoxy)ethanol · additive · 2 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	478	0.65	0.77	50	AKG, FE2, PG0
2	128	0.47	0.78	19	empty
3	59	0.34	0.77	17	empty

Compared structures

5UQD · DPY-21 in complex with Fe(II) and alpha-Ketoglutarate · the same entry in another collection · chain A against A, TM-score 1.00
Q9GRZ3 · AlphaFold monomer V2.0 prediction for lysine-specific demethylase 9 (Q9GRZ3) · 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 Q9GRZ3
Elsewhere: RCSB PDB 5UQD · PDBe 5UQD · UniProt Q9GRZ3

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