7A3F | pdb_00007a3f

Crystal structure of apo DPP9

• PDB DOI: https://doi.org/10.2210/pdb7A3F/pdb

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


• Deposited: 2020-08-18 Released: 2021-06-30 
• Deposition Author(s): Ross, B.H., Huber, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.290 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

Discovery and Development of 4-Oxo-beta-Lactams as Novel Inhibitors of Dipeptidyl Peptidases 8 and 9

Fehr, L., Carvalho, L.A.R., Ross, B.H., Lum, K., Vieira, A.C., Kiefersauer, R., Geiss-Friedlander, R., Kaiser, M., Rodrigues, T., Lucas, S.D., Cravatt, B.F., Huber, R., Moreira, R.

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 411.07 kDa 
• Atom Count: 25,685 
• Modeled Residue Count: 3,155 
• Deposited Residue Count: 3,592 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 9	A [auth B], B [auth A], C, D	898	Homo sapiens	Mutation(s): 0  Gene Names: DPP9, DPRP2 EC: 3.4.14.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q86TI2 (Homo sapiens) Explore Q86TI2  Go to UniProtKB:  Q86TI2
PHAROS:  Q86TI2 GTEx:  ENSG00000142002

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4 (Subject of Investigation/LOI)	E [auth B], G [auth A], I [auth C], J [auth D]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	F [auth B], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.290 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.17	α = 86.56
b = 95.31	β = 102.54
c = 127.196	γ = 102.44

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-06-30 
Deposition Author(s): Ross, B.H., Huber, R.

Revision History  

• Version 1.0: 2021-06-30
  Type: Initial release
  
• Version 1.1: 2024-01-31
  Changes: Data collection, Database references, Refinement description