5EHF | pdb_00005ehf

Laccase from Antrodiella faginea


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.195 (Depositor), 0.197 (DCC) 
  • R-Value Work: 
    0.160 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 
    0.162 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

Structure-function study of two new middle-redox potential laccases from basidiomycetes Antrodiella faginea and Steccherinum murashkinskyi.

Glazunova, O.A.Polyakov, K.M.Moiseenko, K.V.Kurzeev, S.A.Fedorova, T.V.

(2018) Int J Biol Macromol 118: 406-418

  • DOI: https://doi.org/10.1016/j.ijbiomac.2018.06.038
  • Primary Citation Related Structures: 
    5E9N, 5EHF

  • PubMed Abstract: 

    Laccases are multicopper oxidases that catalyze oxidation of a wide range of organic and inorganic substrates accompanied by the reduction of dioxygen to water. The physicochemical and catalytic properties of two new fungal laccases from basidiomycetes Antrodiella faginea (AfL) and Steccherinum murashkinskyi (SmL) with middle redox potential of the T1 copper site were studied. The X-ray structures of AfL and SmL were solved at 1.75 Å and 0.95 Å, respectively. The oxidized state of copper ions in the active site was observed in AfL structure, while the mixture of oxidized and reduced states was observed in SmL structure. These oxidized and reduced states relate to the position of copper ions, their coordination, and nature and position of oxygen ligands. Comparative analysis of the T1 site environment of laccases with known structure allowed us to highlight the six types of the secondary coordination sphere of the T1 copper. The solvent accessible surface area of the conservative region of the secondary coordination sphere of the T1 copper correlates with its the redox potential. It was shown that the laccase classification by the structure of the T1 copper secondary coordination sphere is in agreement to ecophysiological behavior of laccase producing fungi.


  • Organizational Affiliation
    • A. N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky Ave. 33/2, Moscow 119071, Russian Federation. Electronic address: olga.a.glas@gmail.com.

Macromolecule Content 

  • Total Structure Weight: 55.57 kDa 
  • Atom Count: 4,348 
  • Modeled Residue Count: 497 
  • Deposited Residue Count: 497 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Laccase497Antrodiella fagineaMutation(s): 0 
EC: 1.10.3.2
UniProt
Find proteins for A0A0M3U1T9 (Antrodiella faginea)
Explore A0A0M3U1T9 
Go to UniProtKB:  A0A0M3U1T9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M3U1T9
Glycosylation
Glycosylation Sites: 3
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
K [auth A],
L [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU

Query on CU



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
I [auth A],
J [auth A]
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.195 (Depositor), 0.197 (DCC) 
  • R-Value Work:  0.160 (Depositor), 0.161 (DCC) 
  • R-Value Observed: 0.162 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.15α = 90
b = 81.54β = 104.75
c = 78.5γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-23
    Type: Initial release
  • Version 1.1: 2018-08-01
    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
  • Version 2.1: 2024-10-23
    Changes: Data collection, Database references, Structure summary