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Vibrio cholerae oligoribonuclease bound to pga

Analyse Vibrio cholerae oligoribonuclease bound to pga in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6N6E
Type: protein + RNA
Length: 183 residues
Chains: 2
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*A)-3')
EC: 3.1.-.-
UniProt: A0A0H6V4D7
Ligands: NA
Pockets: 2 · best druggability 0.45

Structure

x-ray diffraction · 2 distinct chains · 45% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA exonuclease 2 HOMOLOG,SMALL fragment nuclease (EC 3.1.-.-)	protein	181	45% helix, 18% strand	A0A0H6V4D7
D	RNA (5'-R(PGPA)-3')	rna	2	—	—

Ligands and binding sites

NA · Sodium ion · metal · chains A, D

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	103	0.45	0.79	25	empty
2	68	0.30	0.73	12	empty

Interfaces

1 interface between chains.

A–D · 463 Å² buried · 13 hydrogen bonds · protein-nucleic

Compared structures

6N6E · Vibrio cholerae Oligoribonuclease bound to pGA · the same entry in another collection · 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 A0A0H6V4D7
Elsewhere: RCSB PDB 6N6E · PDBe 6N6E · UniProt A0A0H6V4D7

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