1G6I

Crystal structure of the yeast alpha-1,2-mannosidase with bound 1-deoxymannojirimycin at 1.59 A resolution

• PDB DOI: https://doi.org/10.2210/pdb1G6I/pdb

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


• Deposited: 2000-11-06 Released: 2003-06-24 
• Deposition Author(s): Herscovics, A., Lipari, F., Sleno, B., Romera, P.A., Vallee, F., Yip, P., Howell, P.A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 
  0.253 (Depositor) 
• R-Value Work: 
  0.230 (Depositor) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: in silico

Literature

Structure and function of Class I a1,2-mannosidases involved in glycoprotein biosynthesis.

Herscovics, A., Lipari, F., Sleno, B., Romera, P.A., Vallee, F., Yip, P., Howell, P.A.

(2002) Carbohydrate Bioengineering Interdisciplinary Approaches : 28-33

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 65.2 kDa 
• Atom Count: 4,691 
• Modelled Residue Count: 510 
• Deposited Residue Count: 545 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CLASS I ALPHA-1,2-MANNOSIDASE	A	545	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: MNS1 EC: 3.2.1.113
UniProt
Find proteins for P32906 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32906  Go to UniProtKB:  P32906
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: P32906-1

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-Glycosylation
Glycosylation Resources
GlyTouCan:  G34725OX GlyCosmos:  G34725OX GlyGen:  G34725OX

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[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	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

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
DMJ	F [auth A]	1-DEOXYMANNOJIRIMYCIN C6 H13 N O4 LXBIFEVIBLOUGU-KVTDHHQDSA-N
CA	E [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free:  0.253 (Depositor) 
• R-Value Work:  0.230 (Depositor) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.052	α = 90
b = 89.052	β = 90
c = 153.142	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: 2003-06-24 
Deposition Author(s): Herscovics, A., Lipari, F., Sleno, B., Romera, P.A., Vallee, F., Yip, P., Howell, P.A.

Revision History  

• Version 1.0: 2003-06-24
  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: 2017-02-08
  Changes: Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2024-04-03
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-30
  Changes: Structure summary