2F1B | pdb_00002f1b

GOLGI ALPHA-MANNOSIDASE II COMPLEX WITH (2R,3R,4S,5R)-2-({[(1R)-2-hydroxy-1-phenylethyl]amino}methyl)-5-methylpyrrolidine-3,4-diol

• PDB DOI: https://doi.org/10.2210/pdb2F1B/pdb

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


• Deposited: 2005-11-14 Released: 2006-12-05 
• Deposition Author(s): Kuntz, D.A., Rose, D.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.194 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.173 (Depositor) 

Starting Model: experimental

Literature

Evaluation of docking programs for predicting binding of Golgi alpha-mannosidase II inhibitors: a comparison with crystallography.

Englebienne, P., Fiaux, H., Kuntz, D.A., Corbeil, C.R., Gerber-Lemaire, S., Rose, D.R., Moitessier, N.

(2007) Proteins 69: 160-176

• PubMed: 17557336 
• DOI: https://doi.org/10.1002/prot.21479
• Primary Citation Related Structures: 
  2F18, 2F1A, 2F1B


• PubMed Abstract: 
  

  Golgi alpha-mannosidase II (GMII), a zinc-dependent glycosyl hydrolase, is a promising target for drug development in anti-tumor therapies. Using X-ray crystallography, we have determined the structure of Drosophila melanogaster GMII (dGMII) complexed with three different inhibitors exhibiting IC50's ranging from 80 to 1000 microM. These structures, along with those of seven other available dGMII/inhibitor complexes, were then used as a basis for the evaluation of seven docking programs (GOLD, Glide, FlexX, AutoDock, eHiTS, LigandFit, and FITTED). We found that small inhibitors could be accurately docked by most of the software, while docking of larger compounds (i.e., those with extended aromatic cycles or long aliphatic chains) was more problematic. Overall, Glide provided the best docking results, with the most accurately predicted binding around the active site zinc atom. Further evaluation of Glide's performance revealed its ability to extract active compounds from a benchmark library of decoys.

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Organizational Affiliation: 
• Department of Chemistry, McGill University, Montréal, Québec H3A 2K6, Canada.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 120.37 kDa 
• Atom Count: 9,491 
• 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
alpha-mannosidase II	A	1,045	Drosophila melanogaster	Mutation(s): 0  Gene Names: alpha-Man-II, GmII 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
GB3	D [auth A]	(2R,3R,4S,5R)-2-({[(1R)-2-HYDROXY-1-PHENYLETHYL]AMINO}METHYL)-5-METHYLPYRROLIDINE-3,4-DIOL C14 H22 N2 O3 KHLOMLBNZUMIHX-QKGWFMCXSA-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: 1.45 Å
• R-Value Free:  0.194 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.173 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.433	α = 90
b = 110.578	β = 90
c = 139.89	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-05 
Deposition Author(s): Kuntz, D.A., Rose, D.R.

Revision History  

• Version 1.0: 2006-12-05
  Type: Initial release
  
• Version 1.1: 2007-10-16
  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: 2024-11-20
  Changes: Structure summary