1VCU

Structure of the human cytosolic sialidase Neu2 in complex with the inhibitor DANA

Structural Biology Knowledgebase: 1VCU SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.195

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1VCU

Classification: hydrolase

Total Structure Weight: 86375.80

Macromolecule Entities
Molecule Chains Length Organism Details
Sialidase 2 A, B 382 Homo sapiens EC#: 3.2.1.18 IUBMB
Gene Name(s): NEU2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
C11 H17 N O8
JINJZWSZQKHCIP-UFGQHTETSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EPE
Query on EPE

A, B 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES (Synonym)
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
DAN IC50: 40000 - 90000 nM (99) BindingDB
Ki: 5000 - 140000 nM (99) BindingDB

N/A in BindingMoad
Ki: 140000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.195
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 157.65 α = 90.00
b = 74.00 β = 90.64
c = 77.19 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-03-12
  • Released Date: 2004-11-02
  • Deposition author(s): Chavas, L.M.G., Fusi, P., Tringali, C., Venerando, B., Tettamanti, G., Kato, R., Monti, E., Wakatsuki, S.

Revision History

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