6QZW

DPP8 bound to a dipeptide (MP) from the N-terminus of BRCA2

• PDB DOI: https://doi.org/10.2210/pdb6QZW/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: 3.20 Å
• R-Value Free: 0.225 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Starting Model: experimental

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.

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: 311.21 kDa 
• Atom Count: 20,409 
• Modelled Residue Count: 2,505 
• Deposited Residue Count: 2,700 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 8	A [auth C], B [auth A], C [auth B]	898	Homo sapiens	Mutation(s): 0  Gene Names: DPP8, DPRP1, MSTP097, MSTP135, MSTP141 EC: 3.4.14.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q6V1X1 (Homo sapiens) Explore Q6V1X1  Go to UniProtKB:  Q6V1X1
PHAROS:  Q6V1X1 GTEx:  ENSG00000074603

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	G [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.225 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.73	α = 90
b = 246.074	β = 90
c = 261.812	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