3CZN

Golgi alpha-mannosidase II (D204A nucleophile mutant) in complex with GnMan5Gn

• PDB DOI: https://doi.org/10.2210/pdb3CZN/pdb

• Classification: HYDROLASE
• Organism(s): Drosophila melanogaster
• Expression System: Drosophila melanogaster
• Mutation(s): Yes 


• Deposited: 2008-04-29 Released: 2008-06-24 
• Deposition Author(s): Shah, N., Rose, D.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.197 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 121.18 kDa 
• Atom Count: 9,691 
• Modelled Residue Count: 1,014 
• Deposited Residue Count: 1,045 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-mannosidase 2	A	1,045	Drosophila melanogaster	Mutation(s): 1  Gene Names: alpha-Man-II, GmII EC: 3.2.1.114
UniProt
Find proteins for Q24451 (Drosophila melanogaster) Explore Q24451  Go to UniProtKB:  Q24451

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(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-alpha-D-glucopyranose	B	7		N/A
Glycosylation Resources
GlyTouCan:  G07445YJ GlyCosmos:  G07445YJ GlyGen:  G07445YJ

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.197 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.926	α = 90
b = 109.576	β = 90
c = 138.956	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-24 
Deposition Author(s): Shah, N., Rose, D.R.

Revision History  

• Version 1.0: 2008-06-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2021-10-20
  Changes: Database references, Structure summary