MolNFT v1 · #57039 · protein

Crystal structure of homocitrate synthase from thermus thermophilus complexed with magnesuim ion and alpha-ketoglutarate

2ZYF: “Crystal structure of homocitrate synthase from thermus thermophilus complexed with magnesuim ion and…”. X-ray diffraction, 2 ligands (AKG, MG), 2 pockets (best druggability 0.50). MolNFT v1 #57039 on GenesisL1: 3D structure, binding…

PDB: 2ZYF
Type: protein
Length: 314 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Homocitrate synthase
EC: 2.3.3.14
UniProt: O87198
Ligands: AKG, MG
Pockets: 2 · best druggability 0.50

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Homocitrate synthase (EC 2.3.3.14)	protein	314	47% helix, 17% strand	O87198

Ligands and binding sites

AKG · 2-oxoglutaric acid · ligand · chains A
MG · Magnesium ion · metal · 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	163	0.50	0.78	33	AKG, MG
2	76	0.33	0.75	18	empty

Compared structures

2ZYF · Crystal structure of homocitrate synthase from Thermus thermophilus complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
O87198 · AlphaFold monomer V2.0 prediction for homocitrate synthase (O87198) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 O87198
Elsewhere: RCSB PDB 2ZYF · PDBe 2ZYF · UniProt O87198

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