MolNFT v1 · #166039 · protein

Shya endopeptidase from vibrio cholerae (closed form)

6UE4: “Shya endopeptidase from vibrio cholerae (closed form)”. X-ray diffraction, 1 ligand (ZN), 12 pockets (best druggability 0.78). MolNFT v1 #166039 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6UE4
Type: protein
Length: 705 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Shya endopeptidase
UniProt: Q9KN86
Ligands: ZN
Pockets: 12 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 18% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Shya endopeptidase	protein	354	19% helix, 41% strand	Q9KN86
B	Shya endopeptidase	protein	351	18% helix, 40% strand	Q9KN86

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B
GOL · Glycerol · additive · chains B

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

Pockets

12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	520	0.78	0.85	78	empty
2	387	0.76	0.86	64	empty
3	137	0.63	0.86	28	empty
4	88	0.60	0.88	23	empty
5	57	0.51	0.87	12	empty

Interfaces

1 interface between chains.

A–B · 2225 Å² buried · 33 hydrogen bonds · protein-protein

Compared structures

6UE4 · ShyA Endopeptidase from Vibrio cholerae (Closed form) · 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 Q9KN86
Elsewhere: RCSB PDB 6UE4 · PDBe 6UE4 · UniProt Q9KN86

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