5L9C

Crystal structure of an endoglucanase from Penicillium verruculosum in complex with cellobiose

• PDB DOI: https://doi.org/10.2210/pdb5L9C/pdb

• Classification: HYDROLASE
• Organism(s): Talaromyces verruculosus
• Expression System: Talaromyces verruculosus
• Mutation(s): No 


• Deposited: 2016-06-10 Released: 2017-06-28 
• Deposition Author(s): Nemashkalov, V., Vakhrusheva, A., Tishchenko, S., Gabdulkhakov, A., Kravchenko, O., Gusakov, A., Sinisyn, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.273 
• R-Value Work: 0.226 
• R-Value Observed: 0.229 

Literature

Crystal structure of an endoglucanase from Penicillium verruculosum in complex with cellobiose

Nemashkalov, V., Vakhrusheva, A., Tishchenko, S., Gabdulkhakov, A., Kravchenko, O., Gusakov, A., Sinisyn, A.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 143.04 kDa 
• Atom Count: 11,348 
• Modelled Residue Count: 1,216 
• Deposited Residue Count: 1,256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
endoglucanase	A, B, C, D	314	Talaromyces verruculosus	Mutation(s): 0
UniProt
Find proteins for A0A1U7Q1U3 (Talaromyces verruculosus) Explore A0A1U7Q1U3  Go to UniProtKB:  A0A1U7Q1U3

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	E, F, G	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-glucopyranose-(1-4)-beta-D-glucopyranose	H, I, J, K, L, M, N, O	2		N/A
Glycosylation Resources
GlyTouCan:  G84824ZO GlyCosmos:  G84824ZO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	P [auth C], Q [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900005	H, I, J, K, L, M, N, O	beta-cellobiose	Oligosaccharide / Metabolism

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.273 
• R-Value Work: 0.226 
• R-Value Observed: 0.229 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.33	α = 87.23
b = 73.23	β = 94.17
c = 91.15	γ = 100.52

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-06-28 
Deposition Author(s): Nemashkalov, V., Vakhrusheva, A., Tishchenko, S., Gabdulkhakov, A., Kravchenko, O., Gusakov, A., Sinisyn, A.

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Funding Organization	Location	Grant Number
	Russian Federation	--

Revision History  

• Version 1.0: 2017-06-28
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description, Structure summary