MolNFT v1 · #121163 · protein

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

5HN4 · Homoisocitrate dehydrogenase: “Crystal structure of beta-decarboxylating dehydrogenase (TK0280) from thermococcus kodakarensis complexed…”. X-ray diffraction, 2 ligands (48Y, MN), 2 pockets (best druggability 0.52). MolNFT v1…

PDB: 5HN4
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: 48Y, MN
Pockets: 2 · best druggability 0.52

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Homoisocitrate dehydrogenase	protein	329	45% helix, 20% strand	Q5JFV8

Ligands and binding sites

48Y · (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylic acid · ligand · chains A
MN · Manganese (II) ion · metal · chains A
IMD · Imidazole · additive · chains A
IPA · Isopropyl alcohol · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	101	0.52	0.83	20	empty
2	161	0.45	0.76	21	48Y, MN

Compared structures

5HN4 · 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 5HN4 · PDBe 5HN4 · UniProt Q5JFV8

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