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Glycerol bound form of the B12-independent glycerol dehydratase from clostridium butyricum

Analyse Glycerol bound form of the B12-independent glycerol dehydratase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1R9D
Type: protein
Length: 1,572 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycerol dehydratase
UniProt: Q8GEZ8
Pockets: 17 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 52% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Glycerol dehydratase	protein	786	52% helix, 9% strand	Q8GEZ8

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1009	0.81	0.82	78	empty
2	164	0.63	0.85	30	empty
3	149	0.60	0.84	28	empty
4	176	0.60	0.82	25	empty
5	171	0.56	0.80	24	empty

Interfaces

1 interface between chains.

A–B · 1247 Å² buried · 15 hydrogen bonds · protein-protein

Compared structures

1R9D · Glycerol bound form of the B12-independent glycerol dehydratase from Clostridium butyricum · 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 Q8GEZ8
Elsewhere: RCSB PDB 1R9D · PDBe 1R9D · UniProt Q8GEZ8

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