Research workbench

Drosophila dicer-2 bound to blunt dsrna

Analyse Drosophila dicer-2 bound to blunt dsrna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6BU9
Type: protein + RNA
Length: 440 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dicer-2, isoform a; RNA (5'- R(*GP*GP*AP*GP*GP*UP*AP*GP*UP*AP*GP*GP*UP*UP*GP*UP*AP*UP*AP*G…
EC: 3.1.26.3, 3.6.1.3
UniProt: A1ZAW0
Pockets: 7 · best druggability 0.77

Structure

electron microscopy · 3 distinct chains · 45% helix, 6% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dicer-2, isoform a (EC 3.1.26.3, 3.6.1.3)	protein	399	45% helix, 6% strand	A1ZAW0
B	RNA (5'- R(GPGPAPGPGPUPAPGPUPAPGPGPUPUPGPUPAPUPAPGPUPAP* GP*U)-3')	rna	24	—	—
C	RNA (5'- R(APCPUPAPCPUPAPUPAPCPAPAPCPCPUPAP*C)-3')	rna	17	—	—

Pockets

7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	638	0.77	0.83	81	empty
2	303	0.67	0.82	56	empty
3	438	0.64	0.78	48	empty
4	501	0.54	0.72	32	empty
5	215	0.53	0.78	39	empty

Interfaces

2 interfaces between chains.

B–C · 768 Å² buried · 57 hydrogen bonds · nucleic-nucleic
A–B · 52 Å² buried · 0 hydrogen bonds · protein-nucleic

Compared structures

6BU9 · Drosophila Dicer-2 bound to blunt dsRNA · the same entry in another collection · 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 A1ZAW0
Elsewhere: RCSB PDB 6BU9 · PDBe 6BU9 · UniProt A1ZAW0

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