9HHJ | pdb_00009hhj

ManDH5 E303Q in complex with mannotetraose after co-crystalliztion with mannotetraose at 1.6 angstroms resolution a beta-D-Mannanase of GH5 family from Dictyoglomus thermophilium

PDB DOI: https://doi.org/10.2210/pdb9HHJ/pdb

Classification: HYDROLASE
Organism(s): Dictyoglomus thermophilum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-11-21 Released: 2025-12-03
Deposition Author(s): Sivron, Y., Romano, A., Shoham, Y., Shoham, G.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.83 Å
R-Value Free:
0.202 (Depositor), 0.203 (DCC)
R-Value Work:
0.173 (Depositor), 0.174 (DCC)
R-Value Observed:
0.174 (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

ManDH5 E303Q in complex with mannotetraose after co-crystalliztion with mannotetraose at 1.6 angstroms resolution a beta-D-Mannanase of GH5 family from Dictyoglomus thermophilium

Sivron, Y., Romano, A., Shoham, Y., Shoham, G.

To be published.

Macromolecule Content

Total Structure Weight: 69.17 kDa
Atom Count: 5,236
Modeled Residue Count: 563
Deposited Residue Count: 568
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUF5060 domain-containing protein	A	568	Dictyoglomus thermophilum	Mutation(s): 1 Gene Names: ENW00_02810
UniProt
Find proteins for A0A7C3MIF0 (Dictyoglomus thermophilum) Explore A0A7C3MIF0 Go to UniProtKB: A0A7C3MIF0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A7C3MIF0
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose	B	4		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G51338PC GlyCosmos: G51338PC GlyGen: G51338PC

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
BMA (Subject of Investigation/LOI) Query on BMA Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	beta-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-RWOPYEJCSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	G [auth A], H [auth A], I [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-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]
MLT Query on MLT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	D-MALATE C₄ H₆ O₅ BJEPYKJPYRNKOW-UWTATZPHSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]