6Q8N

GH10 endo-xylanase in complex with xylobiose epoxide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Dynamic and Functional Profiling of Xylan-Degrading Enzymes inAspergillusSecretomes Using Activity-Based Probes.

Schroder, S.P.de Boer, C.McGregor, N.G.S.Rowland, R.J.Moroz, O.Blagova, E.Reijngoud, J.Arentshorst, M.Osborn, D.Morant, M.D.Abbate, E.Stringer, M.A.Krogh, K.B.R.M.Raich, L.Rovira, C.Berrin, J.G.van Wezel, G.P.Ram, A.F.J.Florea, B.I.van der Marel, G.A.Codee, J.D.C.Wilson, K.S.Wu, L.Davies, G.J.Overkleeft, H.S.

(2019) ACS Cent Sci 5: 1067-1078

  • DOI: 10.1021/acscentsci.9b00221
  • Primary Citation of Related Structures:  
    6Q7I, 6Q7J, 6Q8N, 6Q8M, 6QE8

  • PubMed Abstract: 
  • Plant polysaccharides represent a virtually unlimited feedstock for the generation of biofuels and other commodities. However, the extraordinary recalcitrance of plant polysaccharides toward breakdown necessitates a continued search for enzymes that degrade these materials efficiently under defined conditions ...

    Plant polysaccharides represent a virtually unlimited feedstock for the generation of biofuels and other commodities. However, the extraordinary recalcitrance of plant polysaccharides toward breakdown necessitates a continued search for enzymes that degrade these materials efficiently under defined conditions. Activity-based protein profiling provides a route for the functional discovery of such enzymes in complex mixtures and under industrially relevant conditions. Here, we show the detection and identification of β-xylosidases and endo -β-1,4-xylanases in the secretomes of Aspergillus niger , by the use of chemical probes inspired by the β-glucosidase inhibitor cyclophellitol. Furthermore, we demonstrate the use of these activity-based probes (ABPs) to assess enzyme-substrate specificities, thermal stabilities, and other biotechnologically relevant parameters. Our experiments highlight the utility of ABPs as promising tools for the discovery of relevant enzymes useful for biomass breakdown.


    Organizational Affiliation

    Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2300 RA Leiden, The Netherlands.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-xylanaseA, B406Aspergillus aculeatus ATCC 16872Mutation(s): 0 
Gene Names: ASPACDRAFT_127619
EC: 3.2.1.8
UniProt
Find proteins for A0A1L9WG58 (Aspergillus aculeatus (strain ATCC 16872 / CBS 172.66 / WB 5094))
Explore A0A1L9WG58 
Go to UniProtKB:  A0A1L9WG58
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], V [auth B], W [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
HQ8 (Subject of Investigation/LOI)
Query on HQ8

Download Ideal Coordinates CCD File 
KA [auth B], T [auth A](1~{R},2~{S},4~{S},5~{R})-cyclohexane-1,2,3,4,5-pentol
C6 H12 O5
IMPKVMRTXBRHRB-MBMOQRBOSA-N
 Ligand Interaction
XYP (Subject of Investigation/LOI)
Query on XYP

Download Ideal Coordinates CCD File 
LA [auth B], U [auth A]beta-D-xylopyranose
C5 H10 O5
SRBFZHDQGSBBOR-KKQCNMDGSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth B] , BA [auth B] , CA [auth B] , DA [auth B] , E [auth A] , EA [auth B] , F [auth A] , FA [auth B] , 
AA [auth B],  BA [auth B],  CA [auth B],  DA [auth B],  E [auth A],  EA [auth B],  F [auth A],  FA [auth B],  G [auth A],  GA [auth B],  H [auth A],  HA [auth B],  I [auth A],  IA [auth B],  J [auth A],  K [auth A],  L [auth A],  M [auth A],  N [auth A],  O [auth A],  P [auth A],  Q [auth A],  R [auth A],  X [auth B],  Y [auth B],  Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
JA [auth B], S [auth A]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.12α = 90
b = 75.75β = 90
c = 221.99γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/M011151/1

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-05
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary