5N04

X-ray crystal structure of an LPMO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Unliganded and substrate bound structures of the cellooligosaccharide active lytic polysaccharide monooxygenase LsAA9A at low pH.

Frandsen, K.E.H.Poulsen, J.N.Tandrup, T.Lo Leggio, L.

(2017) Carbohydr Res 448: 187-190

  • DOI: https://doi.org/10.1016/j.carres.2017.03.010
  • Primary Citation of Related Structures:  
    5N04, 5N05

  • PubMed Abstract: 

    Lytic polysaccharide monooxygenases (LPMOs) have been found to be key components in microbial (bacterial and fungal) degradation of biomass. They are copper metalloenzymes that degrade polysaccharides oxidatively and act in synergy with glycoside hydrolases. Recently crystallographic studies carried out at pH 5.5 of the LPMO from Lentinus similis belonging to the fungal LPMO family AA9 have provided the first atomic resolution view of substrate-LPMO interactions. The LsAA9A structure presented here determined at pH 3.5 shows significant disorder of the active site in the absence of substrate ligand. Furthermore some differences are also observed in regards to substrate (cellohexaose) binding, although the major interaction with the N-terminal histidine remains unchanged.


  • Organizational Affiliation

    Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Auxiliary activity 9235Panus similisMutation(s): 0 
UniProt
Find proteins for A0A0S2GKZ1 (Panus similis)
Explore A0A0S2GKZ1 
Go to UniProtKB:  A0A0S2GKZ1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0S2GKZ1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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

Download Ideal Coordinates CCD File 
B [auth A]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
O [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
HIC
Query on HIC
A
L-PEPTIDE LINKINGC7 H11 N3 O2HIS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.33α = 90
b = 125.33β = 90
c = 125.33γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Danish Council for Strategic ResearchDenmark12-134922
Danish Council for Strategic ResearchDenmark12-134923

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-29
    Type: Initial release
  • Version 1.1: 2017-06-28
    Changes: Database references
  • Version 1.2: 2017-08-02
    Changes: Database references
  • Version 1.3: 2019-08-14
    Changes: Data collection
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.5: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary