Research workbench

Lt-iib-B5 S74D mutant

Analyse Lt-iib-B5 S74D mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4FNF
Type: protein
Length: 980 residues
Chains: 10
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heat-labile enterotoxin iib, B chain
UniProt: P43529
Pockets: 2 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, E, F, G, H, A, B, C, I, J	Heat-labile enterotoxin iib, B chain	protein	98	30% helix, 40% strand	P43529

Ligands and binding sites

ACT · Acetate ion · additive · 10 copies · chains E, F, G, H, A, B, C, I, J

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1040	0.75	0.78	60	empty
2	1000	0.75	0.78	62	empty

Interfaces

10 interfaces between chains.

E–F · 1218 Å² buried · 16 hydrogen bonds · protein-protein
A–J · 1210 Å² buried · 15 hydrogen bonds · protein-protein
C–I · 1210 Å² buried · 15 hydrogen bonds · protein-protein
D–H · 1207 Å² buried · 16 hydrogen bonds · protein-protein
G–H · 1204 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide (disulfide).

Compared structures

4FNF · LT-IIB-B5 S74D mutant · the same entry in another collection · chain J against J, TM-score 1.00
P43529 · AlphaFold monomer V2.0 prediction for heat-labile enterotoxin iib, B chain (P43529) · a predicted model of the same protein · chain G 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 P43529
Elsewhere: RCSB PDB 4FNF · PDBe 4FNF · UniProt P43529

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