Research workbench

Crystal structure of dapb from corynebacterium glutamicum

Analyse Crystal structure of dapb from corynebacterium glutamicum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5EER
Type: protein
Length: 247 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 4-hydroxy-tetrahydrodipicolinate reductase
EC: 1.17.1.8
UniProt: P40110
Ligands: SO4
Pockets: 1 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8)	protein	247	36% helix, 25% strand	P40110

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	304	0.57	0.76	38	SO4

Compared structures

5EER · Crystal structure of DapB from Corynebacterium glutamicum · the same entry in another collection · chain A against A, TM-score 1.00
P40110 · AlphaFold monomer V2.0 prediction for 4-hydroxy- tetrahydrodipicolinate reductase (P40110) · a predicted model of the same protein · chain A against A, TM-score 0.87

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 P40110
Elsewhere: RCSB PDB 5EER · PDBe 5EER · UniProt P40110

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