Research workbench

E1 dehydrase H220K mutant

Analyse E1 dehydrase H220K mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3BB8
Type: protein
Length: 840 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cdp-4-keto-6-deoxy-D-glucose-3-dehydrase
UniProt: Q57323
Ligands: PLP, BEN
Pockets: 8 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cdp-4-keto-6-deoxy-D-glucose-3-dehydrase	protein	420	43% helix, 16% strand	Q57323

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
BEN · Benzamidine · ligand · 2 copies · chains A, B

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

Pockets

8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	63	0.72	0.98	26	PLP
2	671	0.71	0.78	58	empty
3	317	0.68	0.82	59	PLP
4	268	0.58	0.78	37	empty
5	113	0.34	0.72	23	empty

Interfaces

1 interface between chains.

A–B · 3842 Å² buried · 37 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).

Compared structures

3BB8 · E1 Dehydrase H220K Mutant · 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 Q57323
Elsewhere: RCSB PDB 3BB8 · PDBe 3BB8 · UniProt Q57323

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