MolNFT v1 · #157654 · protein + RNA

Vibrio cholerae oligoribonuclease bound to pgg

6N6A: “Vibrio cholerae oligoribonuclease bound to pgg”. X-ray diffraction, 1 ligand (NA), 2 pockets (best druggability 0.42). MolNFT v1 #157654 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6N6A
Type: protein + RNA
Length: 183 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Oligoribonuclease; RNA (5'-R(P*GP*G)-3')
EC: 3.1.-.-
UniProt: A5F3M7
Ligands: NA
Pockets: 2 · best druggability 0.42

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Oligoribonuclease (EC 3.1.-.-)	protein	181	45% helix, 18% strand	A5F3M7
D	RNA (5'-R(PGPG)-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	76	0.42	0.80	16	empty
2	70	0.32	0.74	14	empty

Interfaces

1 interface between chains.

A–D · 474 Å² buried · 14 hydrogen bonds · protein-nucleic

Compared structures

6N6A · Vibrio cholerae Oligoribonuclease bound to pGG · 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 6N6A · PDBe 6N6A · UniProt A5F3M7

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