Research workbench

Crystal structure of beta-decarboxylating dehydrogenase (TK0280) from thermococcus kodakarensis complexed with mn and isocitrate

Analyse Crystal structure of beta-decarboxylating dehydrogenase (TK0280) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5HN5
Type: protein
Length: 327 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Homoisocitrate dehydrogenase
UniProt: Q5JFV8
Ligands: ICT, MN
Pockets: 2 · best druggability 0.47

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Homoisocitrate dehydrogenase	protein	327	45% helix, 20% strand	Q5JFV8

Ligands and binding sites

ICT · Isocitric acid · ligand · chains A
MN · Manganese (II) ion · metal · chains A
MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	117	0.47	0.79	22	empty
2	118	0.42	0.76	23	ICT, MN

Compared structures

5HN5 · Crystal structure of beta-decarboxylating dehydrogenase (TK0280) from Thermococcus… · 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 Q5JFV8
Elsewhere: RCSB PDB 5HN5 · PDBe 5HN5 · UniProt Q5JFV8

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