3QBJ

Crystal structure of dipeptidyl peptidase IV in complex with inhibitor

Structural Biology Knowledgebase: 3QBJ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.202

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3QBJ

Classification: hydrolase / hydrolase inhibitor

Total Structure Weight: 176063.22

Macromolecule Entities
Molecule Chains Length Organism Details
Dipeptidyl peptidase 4 A, B 748 Homo sapiens EC#: 3.4.14.5 IUBMB
Mutation: N150A, N520A
Gene Name(s): DPP4 Gene View ADCP2 CD26
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NXZ
Query on NXZ

A, B 1-[(3S,4S)-4-amino-1-(6-phenylpyrimidin-4- yl)pyrrolidin-3-yl]piperidin-2-one
C19 H23 N5 O
FHAABBQZMYZFKY-RDJZCZTQSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A, B N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

A BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.202
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 65.75 α = 90.00
b = 69.08 β = 90.00
c = 424.16 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-01-13
  • Released Date: 2012-01-25
  • Deposition author(s): Liu, S.P.

Revision History

No revisions since initial release