Research workbench

beta-amylase from Bacillus cereus var. mycoides in complex with alpha-EPG

Analyse beta-amylase from Bacillus cereus var. mycoides in complex with alpha-EPG in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1J11
Type: protein
Length: 2,064 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2
Source: Bacillus cereus
Molecule: Beta-amylase
EC: 3.2.1.2
UniProt: P36924
Ligands: EPG, CA
Pockets: 19 · best druggability 0.80

Structure

x-ray diffraction · resolution 2 · 1 distinct chain · 37% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Beta-amylase (EC 3.2.1.2)	protein	516	37% helix, 19% strand	P36924

Ligands and binding sites

EPG · (2R)-oxiran-2-ylmethyl alpha-D-glucopyranoside · 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

19 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	1107	0.80	0.82	126	EPG
2	698	0.78	0.83	93	empty
3	276	0.74	0.87	44	EPG
4	366	0.73	0.84	57	EPG
5	298	0.71	0.85	45	EPG

Interfaces

4 interfaces between chains.

C–D · 628 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 610 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 505 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 445 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 4 glycan (disulfide, glycosylation).

Compared structures

1J11 · Beta-amylase from bacillus cereus var. mycoides in complex with alpha- epg · 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 C 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 1J11 · PDBe 1J11 · UniProt P36924

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