1PFQ

crystal structure of human apo dipeptidyl peptidase IV / CD26

• PDB DOI: https://doi.org/10.2210/pdb1PFQ/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2003-05-27 Released: 2003-07-01 
• Deposition Author(s): Oefner, C., D'Arcy, A., Mac Sweeney, A., Pierau, S., Gardiner, R., Dale, G.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.298 
• R-Value Work: 0.254 
• R-Value Observed: 0.256 

Literature

High-resolution structure of human apo dipeptidyl peptidase IV/CD26 and its complex with 1-[([2-[(5-iodopyridin-2-yl)amino]-ethyl]amino)-acetyl]-2-cyano-(S)-pyrrolidine.

Oefner, C., D'Arcy, A., Mac Sweeney, A., Pierau, S., Gardiner, R., Dale, G.E.

(2003) Acta Crystallogr D Biol Crystallogr 59: 1206-1212

• PubMed: 12832764 
• DOI: https://doi.org/10.1107/s0907444903010059
• Primary Citation of Related Structures:  
  1PFQ


• PubMed Abstract: 
  

  Dipeptidyl peptidase IV is a multifunctional type II transmembrane serine protease glycoprotein. The high-resolution crystal structure of the homodimeric human apo dipeptidyl peptidase IV has been determined at 1.9 A resolution. In addition, the structure of the binary complex with 1-[([2-[(5-iodopyridin-2-yl)amino]-ethyl]amino)-acetyl]-2-cyano-(S)-pyrrolidine has been solved, revealing the nature of the covalent interaction with the active-site serine.

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Organizational Affiliation: 

Morphochem AG, Basel, Switzerland. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 170.38 kDa 
• Atom Count: 12,418 
• Modelled Residue Count: 1,453 
• Deposited Residue Count: 1,462 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase IV soluble form	A, B	731	Homo sapiens	Mutation(s): 0  Gene Names: DPP4 OR ADCP2 OR CD26 EC: 3.4.14.5
UniProt & NIH Common Fund Data Resources
Find proteins for P27487 (Homo sapiens) Explore P27487  Go to UniProtKB:  P27487
PHAROS:  P27487 GTEx:  ENSG00000197635
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P27487-1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A], D [auth A], E [auth B], F [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.298 
• R-Value Work: 0.254 
• R-Value Observed: 0.256 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.031	α = 90
b = 118.142	β = 90
c = 184.583	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-07-01 
Deposition Author(s): Oefner, C., D'Arcy, A., Mac Sweeney, A., Pierau, S., Gardiner, R., Dale, G.E.

Revision History  

• Version 1.0: 2003-07-01
  Type: Initial release
  
• Version 1.1: 2008-04-29
  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: Data collection, Derived calculations, Structure summary
• Version 1.4: 2024-11-13
  Changes: Data collection, Database references, Structure summary