3BLB

Crystal structure of Golgi Mannosidase II in complex with swainsonine at 1.3 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb3BLB/pdb

• Classification: HYDROLASE
• Organism(s): Drosophila melanogaster
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2007-12-10 Released: 2008-01-08 
• Deposition Author(s): Kuntz, D.A., Rose, D.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.185 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 

Starting Model: experimental

Literature

Golgi Mannosidase II in complex with swainsonine at 1.3 Angstrom.

Kuntz, D.A., Rose, D.R.

To be published.

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: 120.28 kDa 
• Atom Count: 9,376 
• 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): 0  Gene Names: alpha-Man-II, GmII, CG18802 EC: 3.2.1.114
UniProt
Find proteins for Q24451 (Drosophila melanogaster) Explore Q24451  Go to UniProtKB:  Q24451
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: Q24451-1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
SWA	D [auth A]	1S-8AB-OCTAHYDRO-INDOLIZIDINE-1A,2A,8B-TRIOL C8 H15 N O3 FXUAIOOAOAVCGD-WCTZXXKLSA-N
MRD	E [auth A]	(4R)-2-METHYLPENTANE-2,4-DIOL C6 H14 O2 SVTBMSDMJJWYQN-RXMQYKEDSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SWA	BindingDB:  3BLB	Ki: 3 (nM) from 1 assay(s)
		IC50: 37 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.185 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.767	α = 90
b = 109.662	β = 90
c = 138.9	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-08 
Deposition Author(s): Kuntz, D.A., Rose, D.R.

Revision History  

• Version 1.0: 2008-01-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.4: 2024-10-16
  Changes: Structure summary