MolNFT v1 · #149902 · protein

Crystal structure of exo-GLUCOSIDASE/GLUCOSAMINIDASE VC0615 from vibrio cholerae

6GDT · Endoglucanase-related protein: “Crystal structure of exo-GLUCOSIDASE/GLUCOSAMINIDASE VC0615 from vibrio cholerae”. X-ray diffraction, 20 pockets (best druggability 0.84). MolNFT v1 #149902 on GenesisL1: 3D structure, binding sites…

PDB: 6GDT
Type: protein
Length: 2,826 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Endoglucanase-related protein
UniProt: Q9KUA8
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Endoglucanase-related protein	protein	566	39% helix, 18% strand	Q9KUA8
E	Endoglucanase-related protein	protein	562	40% helix, 18% strand	Q9KUA8

Ligands and binding sites

EDO · 1,2-ethanediol · additive · chains C

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

Pockets

20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	397	0.84	0.92	53	empty
2	1180	0.80	0.81	92	empty
3	772	0.74	0.79	70	empty
4	198	0.67	0.85	25	empty
5	204	0.67	0.85	27	empty

Interfaces

4 interfaces between chains.

A–C · 1013 Å² buried · 11 hydrogen bonds · protein-protein
B–E · 769 Å² buried · 6 hydrogen bonds · protein-protein
B–D · 417 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 367 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

6GDT · Crystal structure of exo-glucosidase/glucosaminidase VC0615 from Vibrio Cholerae · 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 Q9KUA8
Elsewhere: RCSB PDB 6GDT · PDBe 6GDT · UniProt Q9KUA8

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