Research workbench

E1 dehydrase

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

PDB: 3BCX
Type: protein
Length: 840 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cdp-6-deoxy-L-threo-D-glycero-4-hexulose-3-dehydrase
UniProt: Q57174
Ligands: BEN, FE
Pockets: 6 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cdp-6-deoxy-L-threo-D-glycero-4-hexulose-3-dehydrase	protein	421	44% helix, 16% strand	Q57174
B	Cdp-6-deoxy-L-threo-D-glycero-4-hexulose-3-dehydrase	protein	419	43% helix, 16% strand	Q57174

Ligands and binding sites

BEN · Benzamidine · ligand · 3 copies · chains A, B
FE · Fe (III) ion · metal · chains A

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

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	315	0.72	0.85	49	empty
2	277	0.71	0.85	38	empty
3	638	0.69	0.77	55	empty
4	152	0.38	0.72	22	empty
5	128	0.36	0.72	21	empty

Interfaces

1 interface between chains.

A–B · 3824 Å² buried · 37 hydrogen bonds · protein-protein

Compared structures

3BCX · E1 Dehydrase · 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 Q57174
Elsewhere: RCSB PDB 3BCX · PDBe 3BCX · UniProt Q57174

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