3QBJ | pdb_00003qbj

Crystal structure of dipeptidyl peptidase IV in complex with inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3QBJ/pdb

• Classification: hydrolase/hydrolase inhibitor
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 
  0.235 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

Crystal structure of dipeptidyl peptidase IV in complex with inhibitor

Liu, S.P.

To be published.

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: 176.06 kDa 
• Atom Count: 12,183 
• Modeled Residue Count: 1,456 
• Deposited Residue Count: 1,496 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 4	A, B	748	Homo sapiens	Mutation(s): 2  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
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: P27487-1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	4		N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NXZ	H [auth A], J [auth B]	1-[(3S,4S)-4-amino-1-(6-phenylpyrimidin-4-yl)pyrrolidin-3-yl]piperidin-2-one C19 H23 N5 O FHAABBQZMYZFKY-RDJZCZTQSA-N
NAG	F [auth A], G [auth A], I [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: 2.21 Å
• R-Value Free:  0.235 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.751	α = 90
b = 69.082	β = 90
c = 424.16	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-01-25 
Deposition Author(s): Liu, S.P.

Revision History  

• Version 1.0: 2012-01-25
  Type: Initial release
  
• 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: 2024-11-20
  Changes: Data collection, Database references, Structure summary