4X4K

Structure of laccase from Botrytis aclada with full copper content

• PDB DOI: https://doi.org/10.2210/pdb4X4K/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Botrytis aclada
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2014-12-03 Released: 2015-12-09 
• Deposition Author(s): Osipov, E.M., Polyakov, K.M., Tikhonova, T.V., Kittl, R., Shleev, S.V., Ludwig, R., Popov, V.O.
• Funding Organization(s): Russian Foundation for Basic Research, Austrian Science Fund

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.233 
• R-Value Work: 0.181 
• R-Value Observed: 0.184 

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: 67.03 kDa 
• Atom Count: 4,444 
• Modelled Residue Count: 525 
• Deposited Residue Count: 580 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Laccase	A	580	Botrytis aclada	Mutation(s): 0
UniProt
Find proteins for H8ZRU2 (Botrytis aclada) Explore H8ZRU2  Go to UniProtKB:  H8ZRU2

Oligosaccharides

Help

Entity ID: 2
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	B	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	6		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G02763QD GlyCosmos:  G02763QD GlyGen:  G02763QD

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN	N [auth A]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
SO4	O [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CU	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.233 
• R-Value Work: 0.181 
• R-Value Observed: 0.184 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.4	α = 90
b = 113.1	β = 109
c = 79.6	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
Coot	model building
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-12-09 
Deposition Author(s): Osipov, E.M., Polyakov, K.M., Tikhonova, T.V., Kittl, R., Shleev, S.V., Ludwig, R., Popov, V.O.

---

Funding Organization	Location	Grant Number
Russian Foundation for Basic Research	Russian Federation	13-04-12083
Austrian Science Fund	Austria	P25148-B20

Revision History  

• Version 1.0: 2015-12-09
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary