1R9N

Crystal Structure of human dipeptidyl peptidase IV in complex with a decapeptide (tNPY) at 2.3 Ang. Resolution

• PDB DOI: https://doi.org/10.2210/pdb1R9N/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens, Macaca mulatta
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2003-10-30 Released: 2005-03-29 
• Deposition Author(s): Aertgeerts, K., Ye, S., Tennant, M.G., Collins, B., Rogers, J., Sang, B.-C., Skene, R., Webb, D.R., Prasad, G.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.251 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 352.43 kDa 
• Atom Count: 25,627 
• Modelled Residue Count: 2,932 
• Deposited Residue Count: 2,996 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase IV	A, C [auth B], E [auth C], G [auth D]	739	Homo sapiens	Mutation(s): 0  Gene Names: DPP4, ADCP2, 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuropeptide Y	B [auth E], D [auth F], F [auth G], H	10	N/A	Mutation(s): 0
UniProt
Find proteins for Q9XSW6 (Macaca mulatta) Explore Q9XSW6  Go to UniProtKB:  Q9XSW6

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I, J, K, L	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	AA [auth C], BA [auth D], CA [auth D], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth C], Y [auth C], Z [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.251 
• R-Value Work: 0.211 
• R-Value Observed: 0.213 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.606	α = 90
b = 122.701	β = 114.88
c = 145.405	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CCP4	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-29 
Deposition Author(s): Aertgeerts, K., Ye, S., Tennant, M.G., Collins, B., Rogers, J., Sang, B.-C., Skene, R., Webb, D.R., Prasad, G.S.

Revision History  

• Version 1.0: 2005-03-29
  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: 2017-10-11
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-08-23
  Changes: Data collection, Database references, Refinement description, Structure summary