MolNFT v2 · #220872 · protein

Structure of Alistipes sp. Glucoside-3-dehydrogenase AL3

8TDF: “Structure of Alistipes sp. Glucoside-3-dehydrogenase AL3”. X-ray diffraction at 2.1, 1 ligand (NAD), 20 pockets (best druggability 0.81). MolNFT v2 #220872 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 8TDF
Type: protein
Length: 1,808 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.1
Source: Alistipes
Molecule: Dehydrogenase
UniProt: A0A4Y1WH70
Ligands: NAD
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · resolution 2.1 · 1 distinct chain · 30% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Dehydrogenase	protein	452	30% helix, 22% strand	A0A4Y1WH70

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	280	0.81	0.93	53	NAD
2	1021	0.77	0.79	104	empty
3	348	0.77	0.87	60	empty
4	344	0.75	0.86	51	NAD
5	332	0.75	0.87	56	empty

Interfaces

2 interfaces between chains.

A–B · 1775 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 1754 Å² buried · 17 hydrogen bonds · protein-protein

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 A0A4Y1WH70
Elsewhere: RCSB PDB 8TDF · PDBe 8TDF · UniProt A0A4Y1WH70

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