MolNFT v1 · #120298 · protein

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

5GVR · Probable ATP-dependent RNA helicase DDX41: “Crystal structure of the DDX41 dead domain in an apo closed form”. X-ray diffraction, 1 ligand (LMR), 1 pocket (best druggability 0.31). MolNFT v1 #120298 on GenesisL1: 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

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