1DL2

CRYSTAL STRUCTURE OF CLASS I ALPHA-1,2-MANNOSIDASE FROM SACCHAROMYCES CEREVISIAE AT 1.54 ANGSTROM RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1DL2/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 1999-12-08 Released: 2000-02-18 
• Deposition Author(s): Vallee, F., Lipari, F., Yip, P., Herscovics, A., Howell, P.L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.227 
• R-Value Work: 0.209 
• R-Value Observed: 0.209 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 60.95 kDa 
• Atom Count: 4,653 
• Modelled Residue Count: 510 
• Deposited Residue Count: 511 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CLASS I ALPHA-1,2-MANNOSIDASE	A	511	Saccharomyces cerevisiae	Mutation(s): 0  EC: 3.2.1.113
UniProt
Find proteins for P32906 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32906  Go to UniProtKB:  P32906

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	7		N/A
Glycosylation Resources
GlyTouCan:  G34725OX GlyCosmos:  G34725OX GlyGen:  G34725OX

Entity ID: 3
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	C	3		N/A
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.54 Å
• R-Value Free: 0.227 
• R-Value Work: 0.209 
• R-Value Observed: 0.209 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.397	α = 90
b = 88.397	β = 90
c = 153.22	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-02-18 
Deposition Author(s): Vallee, F., Lipari, F., Yip, P., Herscovics, A., Howell, P.L.

Revision History  

• Version 1.0: 2000-02-18
  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 1.3: 2017-08-16
  Changes: Advisory, Refinement description, Source and taxonomy
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary