MolNFT v1 · #54962 · protein

Barley limit dextrinase in complex with alpha-cyclodextrin

2Y5E: “Barley limit dextrinase in complex with alpha-cyclodextrin”. X-ray diffraction, 3 ligands (GLC, CA, IOD), 7 pockets (best druggability 0.69). MolNFT v1 #54962 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2Y5E
Type: protein
Length: 866 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Limit dextrinase
EC: 3.2.1.41
UniProt: O48541
Ligands: GLC, CA, IOD
Pockets: 7 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 32% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Limit dextrinase (EC 3.2.1.41)	protein	866	32% helix, 22% strand	O48541

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 6 copies · chains A
CA · Calcium ion · metal · 2 copies · chains A
IOD · Iodide ion · ion · 8 copies · chains A
GOL · Glycerol · additive · chains A

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

Pockets

7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	118	0.69	0.91	25	empty
2	173	0.68	0.87	37	IOD
3	489	0.64	0.77	54	GLC
4	100	0.58	0.86	22	IOD
5	204	0.56	0.79	46	GOL, IOD

Compared structures

2Y5E · Barley limit dextrinase in complex with alpha-cyclodextrin · 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 O48541
Elsewhere: RCSB PDB 2Y5E · PDBe 2Y5E · UniProt O48541

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