MolNFT v1 · #117896 · protein + RNA

S. cerevisiae DBP5 bound to RNA and mant-ADP BEF3

5ELX · ATP-dependent RNA helicase DBP5: “S. cerevisiae DBP5 bound to RNA and mant-ADP BEF3”. X-ray diffraction, 4 ligands (M2A, BEF, MG), 4 pockets (best druggability 0.62). MolNFT v1 #117896 on GenesisL1: 3D structure, binding sites and…

PDB: 5ELX
Type: protein + RNA
Length: 396 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ATP-dependent RNA helicase DBP5; RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
EC: 3.6.4.13
UniProt: A6ZNQ1
Ligands: M2A, BEF, MG, NO3
Pockets: 4 · best druggability 0.62

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ATP-dependent RNA helicase DBP5 (EC 3.6.4.13)	protein	391	40% helix, 17% strand	A6ZNQ1
B	RNA (5'-R(PUPUPUPUPUPU)-3')	rna	5	—	—

Ligands and binding sites

M2A · [(2~{R},3~{R},4~{R},5~{S})-2-(6-aminopurin-9-yl)-4-oxidanyl-5-[[oxidanyl(phosphonooxy)phosphoryl]oxymethyl]oxolan-3-yl] 2-(methylamino)benzoate · ligand · chains A
BEF · Beryllium trifluoride ion · ligand · chains A
MG · Magnesium ion · metal · 2 copies · chains A
NO3 · Nitrate ion · ion · 2 copies · chains A

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	200	0.62	0.83	36	empty
2	255	0.61	0.80	34	M2A, MG, BEF
3	85	0.35	0.75	19	empty
4	90	0.34	0.74	22	empty

Interfaces

1 interface between chains.

A–B · 721 Å² buried · 24 hydrogen bonds · protein-nucleic

Compared structures

5ELX · S. cerevisiae Dbp5 bound to RNA and mant-ADP BeF3 · the same entry in another collection · chain A against A, TM-score 1.00
A6ZNQ1 · AlphaFold monomer V2.0 prediction for ATP-dependent RNA helicase DBP5 (A6ZNQ1) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 A6ZNQ1
Elsewhere: RCSB PDB 5ELX · PDBe 5ELX · UniProt A6ZNQ1

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