3JYH

Human dipeptidyl peptidase DPP7

• PDB DOI: https://doi.org/10.2210/pdb3JYH/pdb

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


• Deposited: 2009-09-21 Released: 2009-10-13 
• Deposition Author(s): Dobrovetsky, E., Dong, A., Seitova, A., Crombett, L., Paganon, S., Cossar, D., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Weigelt, J., Hassel, A., Shewchuk, L., Bochkarev, A., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.222 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Literature

Human dipeptidyl peptidase DPP7

Dobrovetsky, E., Dong, A., Seitova, A., Crombett, L., Paganon, S., Cossar, D., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Weigelt, J., Hassel, A., Shewchuk, L., Bochkarev, A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 213.38 kDa 
• Atom Count: 15,144 
• Modelled Residue Count: 1,805 
• Deposited Residue Count: 1,876 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl-peptidase 2	A, B, C, D	469	Homo sapiens	Mutation(s): 0  Gene Names: DPP2, DPP7, QPP EC: 3.4.14.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHL4 (Homo sapiens) Explore Q9UHL4  Go to UniProtKB:  Q9UHL4
PHAROS:  Q9UHL4 GTEx:  ENSG00000176978
Glycosylation
Glycosylation Sites: 4		Go to GlyGen: Q9UHL4-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, G, I	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

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	F, H, 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	M [auth A], N [auth A], O [auth B], P [auth C], Q [auth C], R [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.222 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.216	α = 90
b = 130.215	β = 102.36
c = 124.436	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-13 
Deposition Author(s): Dobrovetsky, E., Dong, A., Seitova, A., Crombett, L., Paganon, S., Cossar, D., Edwards, A.M., Arrowsmith, C.H., Bountra, C., Weigelt, J., Hassel, A., Shewchuk, L., Bochkarev, A., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-10-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2024-11-20
  Changes: Data collection, Database references, Structure summary