MolNFT v1 · #10748 · protein

Beta-amylase from bacillus cereus var. mycoides in complex with glucose

1J0Y: “Beta-amylase from bacillus cereus var. mycoides in complex with glucose”. X-ray diffraction, 2 ligands (BGC, CA), 20 pockets (best druggability 0.80). MolNFT v1 #10748 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1J0Y
Type: protein
Length: 2,064 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Beta-amylase
EC: 3.2.1.2
UniProt: P36924
Ligands: BGC, CA
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Beta-amylase (EC 3.2.1.2)	protein	516	38% helix, 19% strand	P36924

Ligands and binding sites

BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
CA · Calcium ion · metal · 4 copies · chains A, B, C, D

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	1081	0.80	0.82	126	BGC
2	731	0.78	0.83	90	empty
3	296	0.75	0.87	37	BGC
4	421	0.74	0.84	59	BGC
5	380	0.73	0.84	48	BGC

Interfaces

4 interfaces between chains.

C–D · 619 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 604 Å² buried · 4 hydrogen bonds · protein-protein
B–D · 484 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 480 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

1J0Y · Beta-amylase from Bacillus cereus var. mycoides in complex with glucose · the same entry in another collection · chain D against D, TM-score 1.00
P36924 · AlphaFold monomer V2.0 prediction for beta-amylase (P36924) · a predicted model of the same protein · 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 P36924
Elsewhere: RCSB PDB 1J0Y · PDBe 1J0Y · UniProt P36924

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