MolNFT v1 · #139688 · protein

Structure of glycerol dehydrogenase crystallised as a contaminant

5XN8: “Structure of glycerol dehydrogenase crystallised as a contaminant”. X-ray diffraction, 1 ligand (ZN), 8 pockets (best druggability 0.74). MolNFT v1 #139688 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5XN8
Type: protein
Length: 1,460 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycerol dehydrogenase
Ligands: ZN
Pockets: 8 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 57% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Glycerol dehydrogenase	protein	365	57% helix, 13% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 2 copies · chains A, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	472	0.74	0.82	50	empty
2	605	0.73	0.80	59	empty
3	590	0.69	0.78	66	ZN
4	595	0.69	0.78	62	GOL
5	552	0.69	0.78	56	empty

Interfaces

3 interfaces between chains.

A–B · 1602 Å² buried · 28 hydrogen bonds · protein-protein
C–D · 1505 Å² buried · 25 hydrogen bonds · protein-protein
A–C · 192 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5XN8 · Structure of glycerol dehydrogenase crystallised as a contaminant · 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
Elsewhere: RCSB PDB 5XN8 · PDBe 5XN8

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