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S. cerevisiae Dbp5 bound to RNA and ADP BeF3

Analyse S. cerevisiae Dbp5 bound to RNA and ADP BeF3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3PEY
Type: protein + RNA
Length: 396 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.401
Source: Saccharomyces cerevisiae; SYNTHETIC CONSTRUCT
Molecule: ATP-dependent RNA helicase DBP5; RNA (5'-R(P*UP*UP*UP*UP*UP*U)-3')
EC: 3.6.4.13
UniProt: P20449
Ligands: ADP, BEF, MG, NO3
Pockets: 4 · best druggability 0.63

Structure

x-ray diffraction · resolution 1.401 · 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	P20449
B	RNA (5'-R(PUPUPUPUPUPU)-3')	rna	5	—	—

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A
BEF · Beryllium trifluoride ion · ligand · chains A
MG · Magnesium ion · metal · 3 copies · chains A
NO3 · Nitrate ion · ion · 4 copies · chains A, B
GOL · Glycerol · additive · 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	266	0.63	0.81	42	ADP, MG, BEF
2	203	0.60	0.82	38	empty
3	89	0.34	0.74	22	empty
4	53	0.33	0.78	20	empty

Interfaces

1 interface between chains.

A–B · 707 Å² buried · 22 hydrogen bonds · protein-nucleic

Compared structures

3PEY · S. cerevisiae DBP5 bound to RNA and ADP BEF3 · the same entry in another collection · chain A against A, TM-score 1.00
P20449 · AlphaFold monomer V2.0 prediction for ATP-dependent RNA helicase DBP5 (P20449) · 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 P20449
Elsewhere: RCSB PDB 3PEY · PDBe 3PEY · UniProt P20449

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