2F1B

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 
• R-Value Work: 0.173 
• R-Value Observed: 0.173 

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 
• 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 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

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

Binding Affinity Annotations
ID	Source	Binding Affinity
GB3	Binding MOAD:  2F1B	IC50: 1.00e+6 (nM) from 1 assay(s)
	PDBBind:  2F1B	IC50: 1.00e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.194 
• R-Value Work: 0.173 
• R-Value Observed: 0.173 
• 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