21JH | pdb_000021jh

Faecalibacterium duncaniae branching enzyme FdBE2 unliganded form

PDB DOI: https://doi.org/10.2210/pdb21JH/pdb

Classification: TRANSFERASE
Organism(s): Faecalibacterium duncaniae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-12-15 Released: 2025-12-31
Deposition Author(s): Tonozuka, T., Ding, Y., Sugimura, R.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.173 (Depositor), 0.178 (DCC)
R-Value Work:
0.149 (Depositor)
R-Value Observed:
0.150 (Depositor)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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

Literature

Enzymatic and Structural Characterization of a Branching Enzyme FdBE2 from the Gut Bacterium Faecalibacterium duncaniae.

Ding, Y., Sugimura, R., Kusama, M., Suzuki, R., Endo, A., Nishikawa, A., Kozono, T., Tonozuka, T.

(2026) J Appl Glycosci (1999)

DOI: https://doi.org/10.5458/jag.7304108

Macromolecule Content

Total Structure Weight: 73.94 kDa
Atom Count: 5,461
Modeled Residue Count: 609
Deposited Residue Count: 637
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1,4-alpha-glucan branching enzyme	A	637	Faecalibacterium duncaniae	Mutation(s): 0 Gene Names: glgB, FAEPRAA2165_01813 EC: 2.4.1.18
UniProt
Find proteins for C7H686 (Faecalibacterium duncaniae) Explore C7H686 Go to UniProtKB: C7H686
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	C7H686
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TRS Query on TRS 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]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
PEG Query on PEG 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]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		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 C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A]	E [auth A] F [auth A] G [auth A] I [auth A] J [auth A] E [auth A], F [auth A], G [auth A], I [auth A], J [auth A], K [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]