MolNFT v1 · #157662 · protein + RNA

Human REXO2 bound to pgg

6N6I · RNA exonuclease 2 HOMOLOG,SMALL fragment nuclease: “Human REXO2 bound to pgg”. X-ray diffraction, 1 ligand (NA), 3 pockets (best druggability 0.54). MolNFT v1 #157662 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6N6I
Type: protein + RNA
Length: 373 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA exonuclease 2 HOMOLOG,SMALL fragment nuclease; RNA (5'-R(P*GP*G)-3')
EC: 3.1.-.-
UniProt: Q9Y3B8
Ligands: NA
Pockets: 3 · best druggability 0.54

Structure

x-ray diffraction · 3 distinct chains · 49% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA exonuclease 2 HOMOLOG,SMALL fragment nuclease (EC 3.1.-.-)	protein	183	49% helix, 18% strand	Q9Y3B8
D, C	RNA (5'-R(PGPG)-3')	rna	2	—	—
B	RNA exonuclease 2 HOMOLOG,SMALL fragment nuclease (EC 3.1.-.-)	protein	186	49% helix, 18% strand	Q9Y3B8

Ligands and binding sites

NA · Sodium ion · metal · 2 copies · chains A, D, B, C
GOL · Glycerol · additive · 2 copies · chains A, D, B
MLI · Malonate ion · additive · chains A, B
EDO · 1,2-ethanediol · additive · chains B, C

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

Pockets

3 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	292	0.54	0.75	33	empty
2	131	0.51	0.80	27	GOL
3	104	0.43	0.78	20	EDO

Interfaces

5 interfaces between chains.

A–B · 1950 Å² buried · 31 hydrogen bonds · protein-protein
B–C · 445 Å² buried · 12 hydrogen bonds · protein-nucleic
A–D · 442 Å² buried · 12 hydrogen bonds · protein-nucleic
A–C · 138 Å² buried · 4 hydrogen bonds · protein-nucleic
D–B · 136 Å² buried · 4 hydrogen bonds · protein-nucleic

Compared structures

6N6I · Human REXO2 bound to pGG · the same entry in another collection · chain A against A, TM-score 1.00
Q9Y3B8 · AlphaFold monomer V2.0 prediction for oligoribonuclease, mitochondrial (Q9Y3B8) · a predicted model of the same protein · 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 Q9Y3B8
Elsewhere: RCSB PDB 6N6I · PDBe 6N6I · UniProt Q9Y3B8

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