3DIV

Crystal structure of laccase from Cerrena maxima at 1.76A resolution

• PDB DOI: https://doi.org/10.2210/pdb3DIV/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Cerrena
• Mutation(s): No 


• Deposited: 2008-06-21 Released: 2009-06-23 
• Deposition Author(s): Lyashenko, A.V., Zhukova, Y.N., Mikhailov, A.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.217 
• R-Value Work: 0.176 
• R-Value Observed: 0.181 

Starting Model: experimental

Literature

Crystal Structure of laccase from Cerrena maxima at 1.76A resolution.

Lyashenko, A.V., Zhukova, Y.N., Mikhailov, A.M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 56.21 kDa 
• Atom Count: 4,645 
• Modelled Residue Count: 499 
• Deposited Residue Count: 499 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LACCASE	A	499	Cerrena	Mutation(s): 0  EC: 1.10.3.2
UniProt
Find proteins for D0VWU3 (Trametes maxima) Explore D0VWU3  Go to UniProtKB:  D0VWU3
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose	D	2		N/A
Glycosylation Resources
GlyTouCan:  G00891MP GlyCosmos:  G00891MP GlyGen:  G00891MP

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	K [auth A], L [auth A], M [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN	E [auth A], F [auth A]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
CU	G [auth A], H [auth A], I [auth A], J [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NIY	A	L-PEPTIDE LINKING	C9 H10 N2 O5		TYR

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900112	D	3alpha-alpha-mannobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 0.217 
• R-Value Work: 0.176 
• R-Value Observed: 0.181 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.581	α = 90
b = 77.101	β = 90
c = 130.884	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-06-23 
Deposition Author(s): Lyashenko, A.V., Zhukova, Y.N., Mikhailov, A.M.

Revision History  

• Version 1.0: 2009-06-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2016-08-24
  Changes: Non-polymer description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary