6QZW | pdb_00006qzw

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free:
0.225 (Depositor), 0.224 (DCC)
R-Value Work:
0.184 (Depositor), 0.187 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6QZW

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

Macromolecules

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6V1X1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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	3D Interactions
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain G [auth C] MOL2 format, chain G [auth C] mmCIF format, chain G [auth C]	G [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth C] Interactions & Density Focus chain G [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.225 (Depositor), 0.224 (DCC)
R-Value Work: 0.184 (Depositor), 0.187 (DCC)
R-Value Observed: 0.186 (Depositor)

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

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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.