MolNFT v1 · #10750 · protein

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

1J10: “Beta-amylase from bacillus cereus var. mycoides in complex with ggx”. X-ray diffraction, 4 ligands (GLC, XYP, XYS), 20 pockets (best druggability 0.80). MolNFT v1 #10750 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1J10
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: GLC, XYP, XYS, 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

GLC · alpha-D-glucopyranose · sugar · 16 copies · chains A, B, C, D
XYP · beta-D-xylopyranose · sugar · 7 copies · chains A, C, B, D
XYS · alpha-D-xylopyranose · sugar · chains C
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, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	905	0.80	0.82	114	GLC
2	556	0.75	0.82	68	empty
3	299	0.65	0.81	41	GLC
4	484	0.64	0.76	43	GLC
5	268	0.63	0.81	41	empty

Interfaces

4 interfaces between chains.

C–D · 684 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 660 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 499 Å² buried · 0 hydrogen bonds · protein-protein
B–D · 486 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

1J10 · beta-amylase from Bacillus cereus var. mycoides in complex with GGX · 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 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 P36924
Elsewhere: RCSB PDB 1J10 · PDBe 1J10 · UniProt P36924

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