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Vibrio cholerae Oligoribonuclease bound to pAA

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

PDB: 6N6C
Type: protein + RNA
Length: 183 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.619
Source: Vibrio cholerae; SYNTHETIC CONSTRUCT
Molecule: RNA exonuclease 2 homolog,Small fragment nuclease; RNA (5'-R(P*AP*A)-3')
EC: 3.1.-.-
UniProt: A5F3M7
Ligands: NA
Pockets: 2 · best druggability 0.44

Structure

x-ray diffraction · resolution 1.619 · 2 distinct chains · 45% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA exonuclease 2 homolog,Small fragment nuclease (EC 3.1.-.-)	protein	181	45% helix, 16% strand	A5F3M7
D	RNA (5'-R(PAPA)-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	0.44	0.79	24	empty
2	70	0.32	0.74	15	empty

Interfaces

1 interface between chains.

A–D · 455 Å² buried · 13 hydrogen bonds · protein-nucleic

Compared structures

6N6C · Vibrio cholerae oligoribonuclease bound to paa · the same entry in another collection · chain A against A, TM-score 1.00
A5F3M7 · AlphaFold monomer V2.0 prediction for oligoribonuclease (A5F3M7) · 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 A5F3M7
Elsewhere: RCSB PDB 6N6C · PDBe 6N6C · UniProt A5F3M7

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