MolNFT v1 · #162554 · protein + DNA

Crystal structure of REXO2-D199A-dada

6RCN · Oligoribonuclease, mitochondrial: “Crystal structure of REXO2-D199A-dada”. X-ray diffraction, 2 ligands (ZN, MG), 3 pockets (best druggability 0.56). MolNFT v1 #162554 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6RCN
Type: protein + DNA
Length: 330 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Oligoribonuclease, mitochondrial; DNA (5'-D(P*AP*A)-3')
EC: 3.1.-.-
UniProt: Q9Y3B8
Ligands: ZN, MG
Pockets: 3 · best druggability 0.56

Structure

x-ray diffraction · 3 distinct chains · 47% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Oligoribonuclease, mitochondrial (EC 3.1.-.-)	protein	180	49% helix, 18% strand	Q9Y3B8
B	Oligoribonuclease, mitochondrial (EC 3.1.-.-)	protein	148	44% helix, 24% strand	Q9Y3B8
C	DNA (5'-D(PAPA)-3')	dna	2	—	—

Ligands and binding sites

ZN · Zinc ion · metal · chains A, C
MG · Magnesium ion · metal · chains A, 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	295	0.56	0.76	38	empty
2	121	0.50	0.81	25	empty
3	83	0.30	0.73	18	empty

Interfaces

3 interfaces between chains.

A–B · 1762 Å² buried · 26 hydrogen bonds · protein-protein
A–C · 433 Å² buried · 10 hydrogen bonds · protein-nucleic
B–C · 130 Å² buried · 1 hydrogen bond · protein-nucleic

Compared structures

6RCN · Crystal structure of REXO2-D199A-dAdA · 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 6RCN · PDBe 6RCN · UniProt Q9Y3B8

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