9SJH | pdb_00009sjh

Crystal structure of apo GHdex dextranase (BT3087), E360A catalytic mutant

PDB DOI: https://doi.org/10.2210/pdb9SJH/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Bacteroides thetaiotaomicron VPI-5482
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): Yes

Deposited: 2025-08-31 Released: 2026-07-29
Deposition Author(s): Feasey, M., Basle, A., van den Berg, B.
Funding Organization(s): Wellcome Trust

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.230 (Depositor), 0.230 (DCC)
R-Value Work:
0.190 (Depositor), 0.190 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Structural and functional characterisation of the dextran utilisome from Bacteroides thetaiotaomicron

Feasey, M., Silale, A., Basle, A., van den Berg, B.

(2026) J Struct Biol X : 100153

DOI: https://doi.org/10.1016/j.yjsbx.2026.100153

Macromolecule Content

Total Structure Weight: 133.21 kDa
Atom Count: 9,950
Modeled Residue Count: 1,138
Deposited Residue Count: 1,154
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cycloisomaltooligosaccharide glucanotransferase	A [auth B], B [auth A]	577	Bacteroides thetaiotaomicron VPI-5482	Mutation(s): 1 Gene Names: BT_3087
UniProt
Find proteins for Q8A368 (Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / JCM 5827 / CCUG 10774 / NCTC 10582 / VPI-5482 / E50)) Explore Q8A368 Go to UniProtKB: Q8A368
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8A368
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain C [auth B] SDF format, chain CA [auth A] SDF format, chain D [auth B] SDF format, chain DA [auth A] SDF format, chain E [auth B] SDF format, chain EA [auth A] SDF format, chain F [auth B] SDF format, chain FA [auth A] SDF format, chain G [auth B] SDF format, chain GA [auth A] SDF format, chain I [auth B] SDF format, chain IA [auth A] SDF format, chain J [auth B] SDF format, chain JA [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth A] SDF format, chain K [auth B] SDF format, chain HA [auth A] SDF format, chain H [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain C [auth B] MOL2 format, chain CA [auth A] MOL2 format, chain D [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain E [auth B] MOL2 format, chain EA [auth A] MOL2 format, chain F [auth B] MOL2 format, chain FA [auth A] MOL2 format, chain G [auth B] MOL2 format, chain GA [auth A] MOL2 format, chain I [auth B] MOL2 format, chain IA [auth A] MOL2 format, chain J [auth B] MOL2 format, chain JA [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain K [auth B] MOL2 format, chain HA [auth A] MOL2 format, chain H [auth B] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain C [auth B] mmCIF format, chain CA [auth A] mmCIF format, chain D [auth B] mmCIF format, chain DA [auth A] mmCIF format, chain E [auth B] mmCIF format, chain EA [auth A] mmCIF format, chain F [auth B] mmCIF format, chain FA [auth A] mmCIF format, chain G [auth B] mmCIF format, chain GA [auth A] mmCIF format, chain I [auth B] mmCIF format, chain IA [auth A] mmCIF format, chain J [auth B] mmCIF format, chain JA [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth A] mmCIF format, chain V [auth A] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain K [auth B] mmCIF format, chain HA [auth A] mmCIF format, chain H [auth B]	AA [auth A] BA [auth A] C [auth B] CA [auth A] D [auth B] AA [auth A], BA [auth A], C [auth B], CA [auth A], D [auth B], DA [auth A], E [auth B], EA [auth A], F [auth B], FA [auth A], G [auth B], GA [auth A], H [auth B], HA [auth A], I [auth B], IA [auth A], J [auth B], JA [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain C [auth B] Focus chain CA [auth A] Focus chain D [auth B] Focus chain DA [auth A] Focus chain E [auth B] Focus chain EA [auth A] Focus chain F [auth B] Focus chain FA [auth A] Focus chain G [auth B] Focus chain GA [auth A] Focus chain H [auth B] Focus chain HA [auth A] Focus chain I [auth B] Focus chain IA [auth A] Focus chain J [auth B] Focus chain JA [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain C [auth B] Focus chain CA [auth A] Focus chain D [auth B] Focus chain DA [auth A] Focus chain E [auth B] Focus chain EA [auth A] Focus chain F [auth B] Focus chain FA [auth A] Focus chain G [auth B] Focus chain GA [auth A] Focus chain H [auth B] Focus chain HA [auth A] Focus chain I [auth B] Focus chain IA [auth A] Focus chain J [auth B] Focus chain JA [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B] mmCIF format, chain P [auth B]	P [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain P [auth B] Interactions & Density Focus chain P [auth B]