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Structural base for cyclodextrin hydrolysis

Analyse Structural base for cyclodextrin hydrolysis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3EDK
Type: protein
Length: 1,194 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyclomaltodextrinase
EC: 3.2.1.54
UniProt: Q8KKG0
Ligands: GLC, CA
Pockets: 10 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cyclomaltodextrinase (EC 3.2.1.54)	protein	597	30% helix, 23% strand	Q8KKG0

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · 16 copies · chains A, B
CA · Calcium ion · metal · 4 copies · chains A, B
GOL · Glycerol · additive · 4 copies · chains A, B

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

Pockets

10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	300	0.63	0.80	45	GLC
2	298	0.61	0.79	46	GLC
3	265	0.60	0.79	40	empty
4	119	0.46	0.78	23	empty
5	72	0.36	0.77	18	empty

Interfaces

1 interface between chains.

A–B · 1717 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

3EDK · Structural base for cyclodextrin hydrolysis · 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 Q8KKG0
Elsewhere: RCSB PDB 3EDK · PDBe 3EDK · UniProt Q8KKG0

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