4I8D

Crystal Structure of Beta-D-glucoside glucohydrolase from Trichoderma reesei

• PDB DOI: https://doi.org/10.2210/pdb4I8D/pdb

• Classification: HYDROLASE
• Organism(s): Trichoderma reesei
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2012-12-03 Released: 2012-12-19 
• Deposition Author(s): Helmich, K.E., Banerjee, G., Bianchetti, C.M., Gudmundsson, M., Sandgren, M., Walton, J.D., Phillips Jr., G.N., Center for Eukaryotic Structural Genomics (CESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.270 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 

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)

Macromolecule Content

• Total Structure Weight: 155.07 kDa 
• Atom Count: 11,388 
• Modelled Residue Count: 1,425 
• Deposited Residue Count: 1,428 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-D-glucoside glucohydrolase	A, B	714	Trichoderma reesei	Mutation(s): 0  Gene Names: AAA18473, bgl1 EC: 3.2.1.21
UniProt
Find proteins for Q12715 (Hypocrea jecorina) Explore Q12715  Go to UniProtKB:  Q12715

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[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, D	8		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G80966KZ GlyCosmos:  G80966KZ GlyGen:  G80966KZ

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
BGC	G [auth A], H [auth B]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.48 Å
• R-Value Free: 0.270 
• R-Value Work: 0.201 
• R-Value Observed: 0.204 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.41	α = 90
b = 107.86	β = 115.59
c = 125.86	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-19 
Deposition Author(s): Helmich, K.E., Banerjee, G., Bianchetti, C.M., Gudmundsson, M., Sandgren, M., Walton, J.D., Phillips Jr., G.N., Center for Eukaryotic Structural Genomics (CESG)

Revision History  

• Version 1.0: 2012-12-19
  Type: Initial release
  
• Version 1.1: 2014-10-22
  Changes: Database references
• Version 1.2: 2014-11-26
  Changes: Database references
• Version 1.3: 2017-11-15
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary