8ZRZ

The 1.26 angstrom resolution structure of Bacillus cereus beta-amylase in complex with maltose

PDB DOI: https://doi.org/10.2210/pdb8ZRZ/pdb

Classification: HYDROLASE
Organism(s): Bacillus cereus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-06-05 Released: 2024-09-25
Deposition Author(s): Mikami, B., Hirata, A.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.26 Å
R-Value Free: 0.165
R-Value Work: 0.124

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Structural insight into sugar-binding modes of microbial beta-amylase.

Hirata, A., Mikami, B.

(2024) Biochem Biophys Res Commun 733

DOI: https://doi.org/10.1016/j.bbrc.2024.150695

Macromolecule Content

Total Structure Weight: 61.45 kDa
Atom Count: 5,480
Modelled Residue Count: 516
Deposited Residue Count: 516
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-amylase	A	516	Bacillus cereus	Mutation(s): 0 Gene Names: spoII EC: 3.2.1.2
UniProt
Find proteins for P36924 (Bacillus cereus) Explore P36924 Go to UniProtKB: P36924
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P36924
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	B [auth C], C [auth F], E [auth D]	2		N/A	Interactions Focus chain B [auth C] Focus chain C [auth F] Focus chain E [auth D] Interactions & Density Focus chain B [auth C] Focus chain C [auth F] Focus chain E [auth D]

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose	D [auth E]	2		N/A	Interactions Focus chain D [auth E] Interactions & Density Focus chain D [auth E]

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	F [auth B]	4		N/A	Interactions Focus chain F [auth B] Interactions & Density Focus chain F [auth B]

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BGC Query on BGC Download Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A]	Q [auth A]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain Q [auth A] Interactions & Density Focus chain Q [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A]	I [auth A] J [auth A] K [auth A] L [auth A] M [auth A] I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A]	G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Biologically Interesting Molecules (External Reference) 2 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001 Query on PRD_900001	B [auth C], C [auth D], E [auth F]	alpha-maltose	Oligosaccharide / Nutrient		Interactions Focus chain B [auth C] Focus chain C [auth F] Focus chain E [auth D] Interactions & Density Focus chain B [auth C] Focus chain C [auth F] Focus chain E [auth D]

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900018 Query on PRD_900018	D [auth E]	beta-maltose	Oligosaccharide / Nutrient		Interactions Focus chain D [auth E] Interactions & Density Focus chain D [auth E]