9GPE | pdb_00009gpe

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/pdb9GPE/pdb

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

Deposited: 2024-09-07 Released: 2025-09-17
Deposition Author(s): Sivron, Y., Romano, A., Shoham, Y., Shoham, G.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free:
0.179 (Depositor), 0.182 (DCC)
R-Value Work:
0.164 (Depositor), 0.169 (DCC)
R-Value Observed:
0.165 (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: 68.25 kDa
Atom Count: 5,335
Modeled Residue Count: 562
Deposited Residue Count: 568
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7C3MIF0
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
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]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900010 Query on PRD_900010	B	alpha-maltotetraose	Oligosaccharide / Substrate analog		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free: 0.179 (Depositor), 0.182 (DCC)
R-Value Work: 0.164 (Depositor), 0.169 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.946	α = 90
b = 99.337	β = 90
c = 153.553	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
xia2	data scaling
PHASER	phasing
Coot	model building

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-09-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2025-09-17
Type: Initial release

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.