6PNR | pdb_00006pnr

A GH31 family sulfoquinovosidase from E. rectale in complex with aza-sugar inhibitor IFGSQ

• PDB DOI: https://doi.org/10.2210/pdb6PNR/pdb

• Classification: Hydrolase/Hydrolas Inhibitor
• Organism(s): Agathobacter rectalis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-07-03 Released: 2020-07-08 
• Deposition Author(s): Jarva, M.A., Lingford, J.P., John, A., Goddard-Borger, E.D.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.217 (Depositor) 
• R-Value Work: 
  0.176 (Depositor) 
• R-Value Observed: 
  0.179 (Depositor) 

Starting Model: experimental

Literature

A GH31 family sulfoquinovosidase from E. rectale in complex with aza-sugar inhibitor IFGSQ

Lingford, J.P., Jarva, M.A., John, A., Goddard-Borger, E.D.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 159.44 kDa 
• Atom Count: 11,860 
• Modeled Residue Count: 1,334 
• Deposited Residue Count: 1,352 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-glucosidase	A, B [auth C]	676	Agathobacter rectalis	Mutation(s): 0  Gene Names: DW001_07735, DW028_04245, DW967_02630 EC: 3.2.1.20
UniProt
Find proteins for C4ZGB7 (Agathobacter rectalis (strain ATCC 33656 / DSM 3377 / JCM 17463 / KCTC 5835 / VPI 0990)) Explore C4ZGB7  Go to UniProtKB:  C4ZGB7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9VH (Subject of Investigation/LOI)	C [auth A], H [auth C]	[(3~{S},4~{R},5~{R})-4,5-bis(oxidanyl)piperidin-3-yl]methanesulfonic acid C6 H13 N O5 S RCSXCFCCYYFFCY-HSUXUTPPSA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A], I [auth C], J [auth C], K [auth C], L [auth C], M [auth C], N [auth C], O [auth C], P [auth C], Q [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.217 (Depositor) 
• R-Value Work:  0.176 (Depositor) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.62	α = 90
b = 122.667	β = 90
c = 126.733	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Currently 6PNR does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2020-07-08 
Deposition Author(s): Jarva, M.A., Lingford, J.P., John, A., Goddard-Borger, E.D.

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Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	GNT1139549

Revision History  

• Version 1.0: 2020-07-08
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary