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Crystal structure of gluconate 5-dehydrogenase from lentibacter algarum

Analyse Crystal structure of gluconate 5-dehydrogenase from lentibacter algarum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6LE3
Type: protein
Length: 990 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gluconate 5-dehydrogenase
UniProt: A0A1H3NGY9
Ligands: ACE
Pockets: 11 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 50% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	Gluconate 5-dehydrogenase	protein	247	51% helix, 15% strand	A0A1H3NGY9
F	Gluconate 5-dehydrogenase	protein	247	49% helix, 15% strand	A0A1H3NGY9
G, H	Gluconate 5-dehydrogenase	protein	248	50% helix, 15% strand	A0A1H3NGY9

Ligands and binding sites

ACE · Acetyl group · ligand · 9 copies · chains E, F, G, H

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1083	0.84	0.85	58	ACE
2	153	0.77	0.94	28	ACE
3	132	0.77	0.95	28	ACE
4	561	0.75	0.82	57	empty
5	282	0.74	0.87	44	ACE

Interfaces

6 interfaces between chains.

G–H · 1598 Å² buried · 24 hydrogen bonds · protein-protein
E–F · 1593 Å² buried · 24 hydrogen bonds · protein-protein
E–G · 1459 Å² buried · 10 hydrogen bonds · protein-protein
F–H · 1437 Å² buried · 11 hydrogen bonds · protein-protein
E–H · 216 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6LE3 · Crystal structure of gluconate 5-dehydrogenase from Lentibacter algarum · the same entry in another collection · chain E against E, 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 A0A1H3NGY9
Elsewhere: RCSB PDB 6LE3 · PDBe 6LE3 · UniProt A0A1H3NGY9

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