5N0F

The catalytic domain, BcGH76, of Bacillus circulans Aman6 in complex with 1,6-ManSIFG

• PDB DOI: https://doi.org/10.2210/pdb5N0F/pdb

• Classification: HYDROLASE
• Organism(s): Niallia circulans
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-02-02 Released: 2017-08-09 
• Deposition Author(s): Jin, Y., Williams, S., Davies, G.
• Funding Organization(s): European Research Council, Australian Research Council

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.218 
• R-Value Work: 0.152 
• R-Value Observed: 0.156 

Starting Model: experimental

Literature

An atypical interaction explains the high-affinity of a non-hydrolyzable S-linked 1,6-alpha-mannanase inhibitor.

Belz, T., Jin, Y., Coines, J., Rovira, C., Davies, G.J., Williams, S.J.

(2017) Chem Commun (Camb) 53: 9238-9241

• PubMed: 28766587 
• DOI: https://doi.org/10.1039/c7cc04977c
• Primary Citation of Related Structures:  
  5M77, 5N0F


• PubMed Abstract: 
  

  The non-hydrolyzable S-linked azasugars, 1,6-α-mannosylthio- and 1,6-α-mannobiosylthioisofagomine, were synthesized and shown to bind with high affinity to a family 76 endo-1,6-α-mannanase from Bacillus circulans. X-ray crystallography showed an atypical interaction of the isofagomine nitrogen with the catalytic acid/base. Molecular dynamics simulations reveal that the atypical binding results from sulfur perturbing the most stable form away from the nucleophile interaction preferred for the O-linked congener.

---

Organizational Affiliation: 

School of Chemistry and Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 82.51 kDa 
• Atom Count: 6,063 
• Modelled Residue Count: 674 
• Deposited Residue Count: 724 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-1,6-mannanase	A, B	362	Niallia circulans	Mutation(s): 1  Gene Names: aman6
UniProt
Find proteins for Q9Z4P9 (Niallia circulans) Explore Q9Z4P9  Go to UniProtKB:  Q9Z4P9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7K2	C [auth A], D [auth B]	[(3S,4R,5R)-4,5-dihydroxypiperidin-3-yl]methyl 1-thio-alpha-D-mannopyranoside C12 H23 N O7 S KDPQETHZRPVZAI-TYMLGRTHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.218 
• R-Value Work: 0.152 
• R-Value Observed: 0.156 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.05	α = 90
b = 86.4	β = 90
c = 103.65	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-08-09 
Deposition Author(s): Jin, Y., Williams, S., Davies, G.

---

Funding Organization	Location	Grant Number
European Research Council	United Kingdom	AdG322942
Australian Research Council	Australia	FT130100103

Revision History  

• Version 1.0: 2017-08-09
  Type: Initial release
  
• Version 1.1: 2017-08-16
  Changes: Database references
• Version 1.2: 2017-08-23
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Author supporting evidence, Derived calculations, Structure summary
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description, Structure summary