MolNFT v1 · #96221 · protein

Structure of tomato bifunctional nuclease TBN1, variant N211D

4JDG: “Structure of tomato bifunctional nuclease TBN1, variant N211D”. X-ray diffraction, 5 ligands (NAG, BMA, MAN), 1 pocket (best druggability 0.35). MolNFT v1 #96221 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4JDG
Type: protein
Length: 266 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nuclease
EC: 3.1.30.-
UniProt: Q0KFV0
Ligands: NAG, BMA, MAN, ZN, PO4
Pockets: 1 · best druggability 0.35

Structure

x-ray diffraction · 1 distinct chain · 64% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Nuclease (EC 3.1.30.-)	protein	266	64% helix, 5% strand	Q0KFV0

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
BMA · beta-D-mannopyranose · sugar · 2 copies · chains A
MAN · alpha-D-mannopyranose · sugar · chains A
ZN · Zinc ion · metal · 3 copies · chains A
PO4 · Phosphate ion · ion · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	85	0.35	0.75	22	ZN, PO4

Modifications

Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

4JDG · Structure of Tomato Bifunctional Nuclease TBN1, variant N211D · 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 Q0KFV0
Elsewhere: RCSB PDB 4JDG · PDBe 4JDG · UniProt Q0KFV0

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.