1KKT

Structure of P. citrinum alpha 1,2-mannosidase reveals the basis for differences in specificity of the ER and Golgi Class I enzymes

• PDB DOI: https://doi.org/10.2210/pdb1KKT/pdb

• Classification: HYDROLASE
• Organism(s): Penicillium citrinum
• Expression System: Aspergillus oryzae
• Mutation(s): No 


• Deposited: 2001-12-10 Released: 2002-01-23 
• Deposition Author(s): Lobsanov, Y.D., Vallee, F., Imberty, A., Yoshida, T., Yip, P., Herscovics, A., Howell, P.L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.239 
• R-Value Work: 0.193 
• R-Value Observed: 0.197 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 116.85 kDa 
• Atom Count: 7,885 
• Modelled Residue Count: 950 
• Deposited Residue Count: 1,022 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mannosyl-oligosaccharide alpha-1,2-mannosidase	A, B	511	Penicillium citrinum	Mutation(s): 0  Gene Names: msdC EC: 3.2.1.113
UniProt
Find proteins for P31723 (Penicillium citrinum) Explore P31723  Go to UniProtKB:  P31723

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

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D, G	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21381MC GlyCosmos:  G21381MC GlyGen:  G21381MC

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	I [auth A], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.239 
• R-Value Work: 0.193 
• R-Value Observed: 0.197 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.487	α = 90
b = 110.997	β = 99.17
c = 86.235	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-01-23 
Deposition Author(s): Lobsanov, Y.D., Vallee, F., Imberty, A., Yoshida, T., Yip, P., Herscovics, A., Howell, P.L.

Revision History  

• Version 1.0: 2002-01-23
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-08-16
  Changes: Data collection, Database references, Refinement description, Structure summary