MolNFT v1 · #121165 · protein

Crystal structure of beta-decarboxylating dehydrogenase (TK0280) from thermococcus kodakarensis complexed with mn and 3-isopropylmalate

5HN6 · Homoisocitrate dehydrogenase: “Crystal structure of beta-decarboxylating dehydrogenase (TK0280) from thermococcus kodakarensis complexed…”. X-ray diffraction, 2 ligands (IPM, MN), 3 pockets (best druggability 0.45). MolNFT v1…

PDB: 5HN6
Type: protein
Length: 329 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Homoisocitrate dehydrogenase
UniProt: Q5JFV8
Ligands: IPM, MN
Pockets: 3 · best druggability 0.45

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Homoisocitrate dehydrogenase	protein	329	42% helix, 20% strand	Q5JFV8

Ligands and binding sites

IPM · 3-isopropylmalic 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

3 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	75	0.45	0.81	17	empty
2	121	0.42	0.76	21	IPM, MN
3	51	0.37	0.80	14	empty

Compared structures

5HN6 · 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 5HN6 · PDBe 5HN6 · UniProt Q5JFV8

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