MolNFT v1 · #67682 · protein + DNA

Crystal structure of a Z-Z junction

3IRQ · Double-stranded RNA-specific adenosine deaminase: “Crystal structure of a Z-Z junction”. X-ray diffraction, 3 pockets (best druggability 0.69). MolNFT v1 #67682 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3IRQ
Type: protein + DNA
Length: 279 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Double-stranded RNA-specific adenosine deaminase; DNA…
EC: 3.5.4.-
UniProt: P55265
Pockets: 3 · best druggability 0.69

Structure

x-ray diffraction · 5 distinct chains · 50% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, C	Double-stranded RNA-specific adenosine deaminase (EC 3.5.4.-)	protein	64	47% helix, 14% strand	P55265
G	DNA (5'-D(GPTPCPGPCPGPCPGPTPCPGPCPGPCP*G)- 3')	dna	14	—	—
F	DNA (5'-D(APCPCPGPCPGPCPGPAPCPGPCPGPCP*G)- 3')	dna	14	—	—
B	Double-stranded RNA-specific adenosine deaminase (EC 3.5.4.-)	protein	62	55% helix, 15% strand	P55265
A	Double-stranded RNA-specific adenosine deaminase (EC 3.5.4.-)	protein	61	49% helix, 11% strand	P55265

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	740	0.69	0.77	48	empty
2	255	0.49	0.74	23	empty
3	106	0.40	0.77	15	empty

Interfaces

9 interfaces between chains.

G–F · 668 Å² buried · 64 hydrogen bonds · nucleic-nucleic
G–B · 408 Å² buried · 5 hydrogen bonds · protein-nucleic
F–C · 393 Å² buried · 7 hydrogen bonds · protein-nucleic
D–F · 374 Å² buried · 7 hydrogen bonds · protein-nucleic
G–A · 369 Å² buried · 6 hydrogen bonds · protein-nucleic

Compared structures

3IRQ · Crystal structure of a Z-Z junction · the same entry in another collection · chain A against A, TM-score 1.00
P55265 · AlphaFold monomer V2.0 prediction for double-stranded RNA-specific adenosine deaminase… · a predicted model of the same protein · chain B against A, TM-score 0.97

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 P55265
Elsewhere: RCSB PDB 3IRQ · PDBe 3IRQ · UniProt P55265

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