MolNFT v1 · #106272 · protein

Crystal structure of a three finger toxin

4RUD · Three-finger toxin 3B: “Crystal structure of a three finger toxin”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.40). MolNFT v1 #106272 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4RUD
Type: protein
Length: 116 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Three-finger toxin 3B
UniProt: U3EPL2
Ligands: ZN
Pockets: 2 · best druggability 0.40

Structure

x-ray diffraction · 1 distinct chain · 0% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Three-finger toxin 3B	protein	58	0% helix, 43% strand	U3EPL2

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B

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	109	0.40	0.76	23	empty
2	71	0.35	0.76	18	empty

Interfaces

1 interface between chains.

A–B · 541 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

4RUD · Crystal structure of a three finger toxin · the same entry in another collection · chain A against A, TM-score 1.00
U3EPL2 · AlphaFold monomer V2.0 prediction for three-finger toxin 3B (U3EPL2) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 U3EPL2
Elsewhere: RCSB PDB 4RUD · PDBe 4RUD · UniProt U3EPL2

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