MolNFT v1 · #54128 · protein

Crystal structure of barley beta-amylase complexed with acarbose

2XFF: “Crystal structure of barley beta-amylase complexed with acarbose”. X-ray diffraction, 3 ligands (AC1, BGC, GLC), 4 pockets (best druggability 0.72). MolNFT v1 #54128 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2XFF
Type: protein
Length: 486 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-amylase
EC: 3.2.1.2
UniProt: P16098
Ligands: AC1, BGC, GLC
Pockets: 4 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Beta-amylase (EC 3.2.1.2)	protein	486	38% helix, 12% strand	P16098

Ligands and binding sites

AC1 · 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose · ligand · chains A
BGC · beta-D-glucopyranose · sugar · chains A
GLC · alpha-D-glucopyranose · sugar · chains A
EDO · 1,2-ethanediol · additive · 2 copies · chains A

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	669	0.72	0.79	64	AC1, EDO
2	131	0.56	0.83	35	empty
3	78	0.34	0.75	19	empty
4	50	0.28	0.75	16	empty

Compared structures

2XFF · Crystal structure of Barley Beta-Amylase complexed with acarbose · the same entry in another collection · chain A against A, TM-score 1.00
P16098 · AlphaFold monomer V2.0 prediction for beta-amylase (P16098) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P16098
Elsewhere: RCSB PDB 2XFF · PDBe 2XFF · UniProt P16098

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