MolNFT v1 · #67676 · protein

Structure of dihydrodipicolinate synthase from clostridium botulinum

3IRD: “Structure of dihydrodipicolinate synthase from clostridium botulinum”. X-ray diffraction, 3 ligands (MLT, NA, CL), 2 pockets (best druggability 0.63). MolNFT v1 #67676 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3IRD
Type: protein
Length: 291 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dihydrodipicolinate synthase
EC: 4.2.1.52
UniProt: A5I6N2
Ligands: MLT, NA, CL
Pockets: 2 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dihydrodipicolinate synthase (EC 4.2.1.52)	protein	291	51% helix, 13% strand	A5I6N2

Ligands and binding sites

MLT · D-malate · ligand · chains A
NA · Sodium ion · metal · chains A
CL · Chloride ion · ion · 2 copies · chains A
GOL · Glycerol · additive · 2 copies · 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	232	0.63	0.82	34	empty
2	78	0.41	0.79	22	MLT

Compared structures

3IRD · Structure of dihydrodipicolinate synthase from Clostridium botulinum · 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 A5I6N2
Elsewhere: RCSB PDB 3IRD · PDBe 3IRD · UniProt A5I6N2

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