MolNFT v1 · #164318 · protein + RNA

Human REXO2 exonuclease in complex with RNA.

6STY · Oligoribonuclease, mitochondrial: “Human REXO2 exonuclease in complex with RNA.”. X-ray diffraction, 1 ligand (CA), 5 pockets (best druggability 0.66). MolNFT v1 #164318 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6STY
Type: protein + RNA
Length: 771 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Oligoribonuclease, mitochondrial; RNA (5'-R(P*AP*UP*C)-3')
EC: 3.1.-.-
UniProt: Q9Y3B8
Ligands: CA
Pockets: 5 · best druggability 0.66

Structure

x-ray diffraction · 6 distinct chains · 49% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Oligoribonuclease, mitochondrial (EC 3.1.-.-)	protein	198	46% helix, 18% strand	Q9Y3B8
B	Oligoribonuclease, mitochondrial (EC 3.1.-.-)	protein	190	49% helix, 18% strand	Q9Y3B8
C	RNA (5'-R(PAPUP*C)-3')	rna	3	—	—
D	Oligoribonuclease, mitochondrial (EC 3.1.-.-)	protein	197	49% helix, 20% strand	Q9Y3B8
E	Oligoribonuclease, mitochondrial (EC 3.1.-.-)	protein	181	50% helix, 22% strand	Q9Y3B8
F	RNA (5'-R(PAPUP*C)-3')	rna	2	—	—

Ligands and binding sites

CA · Calcium ion · metal · chains B, C

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

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	622	0.66	0.76	65	empty
2	127	0.61	0.86	24	empty
3	279	0.60	0.79	38	empty
4	309	0.54	0.75	32	empty
5	71	0.44	0.82	21	empty

Interfaces

6 interfaces between chains.

A–B · 1916 Å² buried · 24 hydrogen bonds · protein-protein
D–E · 1903 Å² buried · 21 hydrogen bonds · protein-protein
B–C · 439 Å² buried · 10 hydrogen bonds · protein-nucleic
E–F · 377 Å² buried · 14 hydrogen bonds · protein-nucleic
A–C · 115 Å² buried · 3 hydrogen bonds · protein-nucleic

Compared structures

6STY · Human REXO2 exonuclease in complex with RNA. · the same entry in another collection · chain E against E, TM-score 1.00
Q9Y3B8 · AlphaFold monomer V2.0 prediction for oligoribonuclease, mitochondrial (Q9Y3B8) · a predicted model of the same protein · chain E 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 6STY · PDBe 6STY · UniProt Q9Y3B8

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