6QZV

DPP9 bound to a dipeptide (MP) from the N-terminus of BRCA2

• PDB DOI: https://doi.org/10.2210/pdb6QZV/pdb

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


• Deposited: 2019-03-12 Released: 2020-09-30 
• Deposition Author(s): Ross, B., Geiss-Friedlander, R., Huber, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.345 
• R-Value Work: 0.286 
• R-Value Observed: 0.289 

Literature

Dipeptidyl peptidase 9 triggers BRCA2 degradation by the N-degron pathway to promote DNA-damage repair

Silva-Garcia, M., Bolgi, O., Ross, B., Pilla, E., Kari, V., Killisch, M., Stark, N., Lenz, C., Spitzner, M., Gorrell, M.D., Grade, M., Urlaub, H., Dobbelstein, M., Huber, R., Geiss-Friedlander, R.

(2020) Biorxiv 

• DOI: https://doi.org/10.1101/2020.08.24.265033

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: 411.49 kDa 
• Atom Count: 26,316 
• Modelled Residue Count: 3,241 
• Deposited Residue Count: 3,600 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 9	A, B, 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MET-PRO	E, F, G, H	2	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.345 
• R-Value Work: 0.286 
• R-Value Observed: 0.289 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.516	α = 90
b = 117.219	β = 105.72
c = 163.401	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-09-30 
Deposition Author(s): Ross, B., Geiss-Friedlander, R., Huber, R.

Revision History  

• Version 1.0: 2020-09-30
  Type: Initial release
  
• Version 1.1: 2021-04-14
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description