Research workbench

Crystal structure of the DDX41 dead domain in an apo closed form

Analyse Crystal structure of the DDX41 dead domain in an apo closed form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5GVR
Type: protein
Length: 234 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Probable ATP-dependent RNA helicase DDX41
EC: 3.6.4.13
UniProt: Q9UJV9
Ligands: LMR
Pockets: 1 · best druggability 0.31

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Probable ATP-dependent RNA helicase DDX41 (EC 3.6.4.13)	protein	234	43% helix, 15% strand	Q9UJV9

Ligands and binding sites

LMR · (2S)-2-hydroxybutanedioic acid · ligand · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	66	0.31	0.74	18	LMR

Compared structures

5GVR · Crystal structure of the DDX41 DEAD domain in an apo closed form · the same entry in another collection · chain A against A, TM-score 1.00
Q9UJV9 · AlphaFold monomer V2.0 prediction for probable ATP-dependent RNA helicase DDX41 (Q9UJV9) · 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 Q9UJV9
Elsewhere: RCSB PDB 5GVR · PDBe 5GVR · UniProt Q9UJV9

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.