6YDE

X-ray structure of LPMO

• PDB DOI: https://doi.org/10.2210/pdb6YDE/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Achaetomiella virescens
• Expression System: Aspergillus oryzae
• Mutation(s): No 


• Deposited: 2020-03-20 Released: 2020-09-16 
• Deposition Author(s): Tandrup, T., Tryfona, T., Frandsen, K.E.H., Johansen, K.S., Dupree, P., Lo Leggio, L.
• Funding Organization(s): Novo Nordisk Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.264 
• R-Value Work: 0.194 
• R-Value Observed: 0.198 

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: 28.94 kDa 
• Atom Count: 2,011 
• Modelled Residue Count: 224 
• Deposited Residue Count: 252 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LPMO lytic polysaccharide monooxygenase	A	252	Achaetomiella virescens	Mutation(s): 0  Gene Names: aa9
UniProt
Find proteins for A0A223GEC9 (Collariella virescens) Explore A0A223GEC9  Go to UniProtKB:  A0A223GEC9

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	B	6		N/A
Glycosylation Resources
GlyTouCan:  G09454VW GlyCosmos:  G09454VW GlyGen:  G09454VW

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CU (Subject of Investigation/LOI)	D [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC	A	L-PEPTIDE LINKING	C7 H11 N3 O2		HIS

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900020	B	beta-cellohexaose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.264 
• R-Value Work: 0.194 
• R-Value Observed: 0.198 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.55	α = 90
b = 124.37	β = 90
c = 51.67	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-09-16 
Deposition Author(s): Tandrup, T., Tryfona, T., Frandsen, K.E.H., Johansen, K.S., Dupree, P., Lo Leggio, L.

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Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NNF17SA0027704

Revision History  

• Version 1.0: 2020-09-16
  Type: Initial release
  
• Version 1.1: 2020-09-23
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description