1R34 | pdb_00001r34

Golgi alpha-mannosidase II complex with 5-thio-D-mannopyranosylamidinium salt

• PDB DOI: https://doi.org/10.2210/pdb1R34/pdb

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


• Deposited: 2003-09-30 Released: 2004-11-02 
• Deposition Author(s): Kuntz, D.A., Xin, W., Kavelekar, L.M., Rose, D.R., Pinto, B.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.196 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

5-Thio-d-glycopyranosylamines and their amidinium salts as potential transition-state mimics of glycosyl hydrolases: synthesis, enzyme inhibitory activities, X-ray crystallography, and molecular modeling

Kavelekar, L.M., Kuntz, D.A., Xin, W., Johnston, B.D., Svensson, B., Rose, D.R., Pinto, B.M.

(2005) Tetrahedron Asymmetry 16: 1035-1046

• DOI: https://doi.org/10.1016/j.tetasy.2005.01.021

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 120.42 kDa 
• Atom Count: 9,283 
• Modeled Residue Count: 1,014 
• Deposited Residue Count: 1,045 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative golgi alpha-mannosidase II	A	1,045	Drosophila melanogaster	Mutation(s): 0  Gene Names: ALPHA-MAN-II 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
LKS	D [auth A]	N-[(1Z)-2-phenylethanimidoyl]-5-thio-alpha-D-mannopyranosylamine C14 H20 N2 O4 S WKJQYOUTPMBFSL-CYDRSHDDSA-N
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MPD	E [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.196 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.774	α = 90
b = 109.568	β = 90
c = 138.737	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: 2004-11-02 
Deposition Author(s): Kuntz, D.A., Xin, W., Kavelekar, L.M., Rose, D.R., Pinto, B.M.

Revision History  

• Version 1.0: 2004-11-02
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.5: 2024-11-13
  Changes: Structure summary