9J4B | pdb_00009j4b

Crystal structure of thio-glucose complexed GH1 beta-glucosidase (UnBGl1)

PDB DOI: https://doi.org/10.2210/pdb9J4B/pdb

Classification: HYDROLASE
Organism(s): soil metagenome
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-08-09 Released: 2026-02-04
Deposition Author(s): Suryawanshi, A.B., Bedi, R.K., Bhaumik, P.
Funding Organization(s): Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free:
0.181 (Depositor), 0.191 (DCC)
R-Value Work:
0.147 (Depositor), 0.162 (DCC)
R-Value Observed:
0.149 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Rewiring Catalytic Craters: A Path for Engineering beta-Glucosidases to Improve Glucose Tolerance

Suryawanshi, A.B., Bedi, R.K., Pawar, M., Noronha, S., Bhaumik, P.

(2025) bioRxiv

DOI: https://doi.org/10.1101/2025.01.02.631061

Macromolecule Content

Total Structure Weight: 53.48 kDa
Atom Count: 4,159
Modeled Residue Count: 457
Deposited Residue Count: 477
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-glucosidase	A	477	soil metagenome	Mutation(s): 0 EC: 3.2.1.21
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GS1 (Subject of Investigation/LOI) Query on GS1 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	1-thio-beta-D-glucopyranose C₆ H₁₂ O₅ S JUSMHIGDXPKSID-DVKNGEFBSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A], F [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A], I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]