3BVX

GOLGI MANNOSIDASE II D204A catalytic nucleophile mutant complex with Methyl (2-deoxy-2-acetamido-beta-D-glucopyranosyl)-(1->2)-(alpha-D-mannopyranosyl)- (1->3)-[(alpha-D-mannopyranosyl)-(1->6)-(alpha-D-mannopyranosyl)-(1->6)]-beta-D-mannopyranoside

Structural Biology Knowledgebase: 3BVX SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.190
  • R-Value Work: 0.153

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3BVX

Classification: HYDROLASE

Total Structure Weight: 120725.77

Macromolecule Entities
Molecule Chains Length Organism Details
Alpha-mannosidase 2 A 1045 Drosophila melanogaster EC#: 3.2.1.114 IUBMB
Fragment: Catalytic domain; UNP residues 76-1108
Mutation: D204A, E907K
Gene Name(s): alpha-Man-II GmII CG18802

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
WZ5
Query on WZ5

A methyl 2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl- (1->2)-alpha-D-mannopyranosyl-(1->3)-[alpha- D-mannopyranosyl-(1->6)-alpha-D-mannopyranosyl- (1->6)]-beta-D-mannopyranoside
Methyl(2-deoxy-2-acetamido-beta-D-glucopyranosyl)- (1->2)-(alpha-D-mannopyranosyl)-(1->3)-[(alpha- D-mannopyranosyl)-(1->6)-(alpha-D-mannopyranosyl)- (1->6)]-beta-D-mannopyranoside (Synonym)
C33 H57 N O26
RVQCIQKGGOSYRW-SDSYCMILSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MPD
Query on MPD

A (4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.190
  • R-Value Work: 0.153
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 68.81 α = 90.00
b = 109.55 β = 90.00
c = 138.52 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-01-07
  • Released Date: 2008-07-01
  • Deposition author(s): Kuntz, D.A., Rose, D.R.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4