9FBE | pdb_00009fbe

3-keto-glycoside eliminase/hydratase in komplex with 2-hydroxy-3-keto-glucal

PDB DOI: https://doi.org/10.2210/pdb9FBE/pdb

Classification: LYASE
Organism(s): Bacteroides thetaiotaomicron
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2024-05-13 Released: 2025-10-29
Deposition Author(s): Pfeiffer, M., Kastner, K., Oberdorfer, G., Nidetzky, B.
Funding Organization(s): Austrian Science Fund

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free:
0.214 (Depositor), 0.216 (DCC)
R-Value Work:
0.170 (Depositor), 0.171 (DCC)
R-Value Observed:
0.172 (Depositor)

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

3-keto-glycoside eliminase/hydratase in komplex with alpha-3-keto-glucose

Pfeiffer, M., Oberdorfer, G., Nidetzky, B., Kastner, K.

To be published.

Macromolecule Content

Total Structure Weight: 62.35 kDa
Atom Count: 4,612
Modeled Residue Count: 511
Deposited Residue Count: 550
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable secreted glycosyl hydrolase	A [auth B], B [auth A]	275	Bacteroides thetaiotaomicron	Mutation(s): 0 Gene Names: BT_2157 EC: 3.2.1.218
UniProt
Find proteins for Q8A5T1 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A5T1 Go to UniProtKB: Q8A5T1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8A5T1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLC Query on GLC Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	alpha-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-DVKNGEFBSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
A1IBU (Subject of Investigation/LOI) Query on A1IBU Download Ideal Coordinates CCD File SDF format, chain C [auth B] SDF format, chain F [auth A] MOL2 format, chain C [auth B] MOL2 format, chain F [auth A] mmCIF format, chain C [auth B] mmCIF format, chain F [auth A]	C [auth B], F [auth A]	2-hydroxy-3-keto-glucal C₆ H₈ O₅ CLDKGBMTBWSEPC-INEUFUBQSA-N		Interactions Focus chain C [auth B] Focus chain F [auth A] Interactions & Density Focus chain C [auth B] Focus chain F [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain D [auth B] MOL2 format, chain G [auth A] MOL2 format, chain D [auth B] mmCIF format, chain G [auth A] mmCIF format, chain D [auth B]	D [auth B], G [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth B] Focus chain G [auth A] Interactions & Density Focus chain D [auth B] Focus chain G [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain E [auth B] MOL2 format, chain I [auth A] MOL2 format, chain E [auth B] mmCIF format, chain I [auth A] mmCIF format, chain E [auth B]	E [auth B], I [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain I [auth A] Interactions & Density Focus chain E [auth B] Focus chain I [auth A]