MolNFT v1 · #35750 · protein

Structure of TT0495 protein from thermus thermophilus

2EKP · 2-deoxy-D-gluconate 3-dehydrogenase: “Structure of TT0495 protein from thermus thermophilus”. X-ray diffraction, 1 ligand (NAD), 1 pocket (best druggability 0.73). MolNFT v1 #35750 on GenesisL1: 3D structure, binding sites and…

PDB: 2EKP
Type: protein
Length: 238 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 2-deoxy-D-gluconate 3-dehydrogenase
EC: 1.1.1.125
UniProt: Q53W82
Ligands: NAD
Pockets: 1 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	2-deoxy-D-gluconate 3-dehydrogenase (EC 1.1.1.125)	protein	238	49% helix, 16% strand	Q53W82

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 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

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	350	0.73	0.84	43	NAD

Compared structures

2EKP · Structure of TT0495 protein from Thermus thermophilus · 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 Q53W82
Elsewhere: RCSB PDB 2EKP · PDBe 2EKP · UniProt Q53W82

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