8WN6 | pdb_00008wn6

Crystal structure of GH1 beta-glucosidase Td2F2 E352Q sophorose complex

PDB DOI: https://doi.org/10.2210/pdb8WN6/pdb

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

Deposited: 2023-10-05 Released: 2025-01-15
Deposition Author(s): Lin, C.C., Lu, T.J., Fushinobu, S.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free:
0.193 (Depositor), 0.208 (DCC)
R-Value Work:
0.165 (Depositor), 0.180 (DCC)
R-Value Observed:
0.166 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 8WN6

This is version 1.1 of the entry. See complete history.

Literature

Structural insights into glycoside hydrolase family 1 beta-glucosidase: Selective oligosaccharide hydrolysis, synthesis, and product profiling.

Lin, C.-C., Uno, H., Yamada, C., Terada, T., Lu, T.-J., Fushinobu, S.

(2026) J Biological Chem

DOI: https://doi.org/10.1016/j.jbc.2026.111293

Macromolecule Content

Total Structure Weight: 52.68 kDa
Atom Count: 3,787
Modeled Residue Count: 441
Deposited Residue Count: 465
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-glucosidase Td2F2	A	465	metagenomes	Mutation(s): 0 EC: 3.2.1.21

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-glucopyranose-(1-2)-beta-D-glucopyranose	B [auth C], C [auth B]	2		N/A	Interactions Focus chain B [auth C] Focus chain C [auth B] Interactions & Density Focus chain B [auth C] Focus chain C [auth B]
Glycosylation Resources
GlyTouCan: G26080VZ GlyCosmos: G26080VZ

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NHE Query on NHE Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C₈ H₁₇ N O₃ S MKWKNSIESPFAQN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
MLA Query on MLA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free: 0.193 (Depositor), 0.208 (DCC)
R-Value Work: 0.165 (Depositor), 0.180 (DCC)
R-Value Observed: 0.166 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.542	α = 90
b = 68.978	β = 90
c = 96.389	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-01-15

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-01-15
Type: Initial release
Version 1.1: 2026-02-25
Changes: Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.