2F25

Crystal Structure of the Human Sialidase Neu2 E111Q Mutant in Complex with DANA Inhibitor

Structural Biology Knowledgebase: 2F25 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.222
  • R-Value Work: 0.192

Literature

Macromolecules
Sequence Display for 2F25

Classification: hydrolase

Total Structure Weight: 86373.83

Macromolecule Entities
Molecule Chains Length Organism Details
Sialidase 2 A, B 382 Homo sapiens EC#: 3.2.1.18 IUBMB
Mutation: E111Q
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 NGL
 
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 NGL
 
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
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.222
  • R-Value Work: 0.192
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 157.37 α = 90.00
b = 73.64 β = 90.31
c = 78.95 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-11-15
  • Released Date: 2006-11-21
  • Deposition author(s): Chavas, L.M.G., Kato, R., Fusi, P., Tringali, C., Venerando, B., Tettamanti, G., Monti, E., Wakatsuki, S.

Revision History

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