6QZV | pdb_00006qzv

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.345 (Depositor), 0.344 (DCC)
R-Value Work:
0.286 (Depositor), 0.287 (DCC)
R-Value Observed:
0.289 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6QZV

This is version 1.2 of the entry. See complete history.

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

Macromolecule Content

Total Structure Weight: 411.49 kDa
Atom Count: 26,316
Modeled Residue Count: 3,241
Deposited Residue Count: 3,600
Unique protein chains: 2

Macromolecules

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q86TI2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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 (Depositor), 0.344 (DCC)
R-Value Work: 0.286 (Depositor), 0.287 (DCC)
R-Value Observed: 0.289 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2020-09-30

Deposition Author(s):

Geiss-Friedlander, R.

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.