Glc(beta-1-3)Glc disaccharide in -1 and -2 sites of Laminarinase 16A from Phanerochaete chrysosporium

Experimental Data Snapshot

  • Resolution: 1.10 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.138 

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This is version 2.1 of the entry. See complete history


X-Ray Crystal Structures of Phanerochaete Chrysosporium Laminarinase 16A in Complex with Products from Lichenin and Laminarin Hydrolysis

Vasur, J.Kawai, R.Andersson, E.Igarashi, K.Sandgren, M.Samejima, M.Stahlberg, J.

(2009) FEBS J 276: 3858

  • DOI: https://doi.org/10.1111/j.1742-4658.2009.07099.x
  • Primary Citation of Related Structures:  
    2W39, 2W52

  • PubMed Abstract: 

    The 1,3(4)-beta-D-glucanases of glycoside hydrolase family 16 provide useful examples of versatile yet specific protein-carbohydrate interactions. In the present study, we report the X-ray structures of the 1,3(4)-beta-D-glucanase Phanerochaete chrysosporium Laminarinase 16A in complex with beta-glucan products from laminarin (1.6 A) and lichenin (1.1 A) hydrolysis. The G6G3G3G glucan, in complex with the enzyme, showed a beta-1,6 branch in the acceptor site. The G4G3G ligand-protein complex showed that there was no room for a beta-1,6 branch in the -1 or -2 subsites; furthermore, the distorted residue in the -1 subsite and the glucose in the -2 subsite required a beta-1,3 bond between them. These are the first X-ray crystal structures of any 1,3(4)-beta-D-glucanase in complex with glucan products. They provide details of both substrate and product binding in support of earlier enzymatic evidence.

  • Organizational Affiliation

    Department of Molecular Biology, University of Agricultural Sciences, Uppsala, Sweden.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PUTATIVE LAMINARINASE298Phanerodontia chrysosporiumMutation(s): 0 
Find proteins for Q874E3 (Phanerodontia chrysosporium)
Explore Q874E3 
Go to UniProtKB:  Q874E3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ874E3
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G36535HU
GlyCosmos:  G36535HU
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAG

Download Ideal Coordinates CCD File 
C [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
Query on LGC

Download Ideal Coordinates CCD File 
D [auth A]D-glucono-1,5-lactone
C6 H10 O6
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Resolution: 1.10 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.138 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.147α = 90
b = 46.713β = 90
c = 152.55γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-21
    Type: Initial release
  • Version 1.1: 2011-08-17
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2023-12-13
    Changes: Data collection, Database references, Refinement description, Structure summary