Research workbench

Human REXO2 bound to pag

Analyse Human REXO2 bound to pag in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6N6K
Type: protein + RNA
Length: 385 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*AP*G)-3')
EC: 3.1.-.-
UniProt: Q9Y3B8
Ligands: NA
Pockets: 3 · best druggability 0.52

Structure

x-ray diffraction · 3 distinct chains · 50% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA exonuclease 2 HOMOLOG,SMALL fragment nuclease (EC 3.1.-.-)	protein	195	51% helix, 17% strand	Q9Y3B8
D, C	RNA (5'-R(PAPG)-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
MLI · Malonate ion · additive · chains A, B

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

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	266	0.52	0.75	33	empty
2	93	0.49	0.82	18	empty
3	84	0.45	0.81	18	NA

Interfaces

5 interfaces between chains.

A–B · 1928 Å² buried · 31 hydrogen bonds · protein-protein
A–D · 458 Å² buried · 13 hydrogen bonds · protein-nucleic
B–C · 445 Å² buried · 12 hydrogen bonds · protein-nucleic
D–B · 138 Å² buried · 3 hydrogen bonds · protein-nucleic
A–C · 135 Å² buried · 3 hydrogen bonds · protein-nucleic

Compared structures

6N6K · Human REXO2 bound to pAG · 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 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 Q9Y3B8
Elsewhere: RCSB PDB 6N6K · PDBe 6N6K · UniProt Q9Y3B8

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.