6ZLX

The structure of the ClpX-associated factor PDIP38

• PDB DOI: https://doi.org/10.2210/pdb6ZLX/pdb

• Classification: CELL CYCLE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-07-01 Released: 2021-07-14 
• Deposition Author(s): Zeth, K., Dougan, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.39 Å
• R-Value Free: 0.287 
• R-Value Work: 0.247 
• R-Value Observed: 0.249 

Literature

PDIP38 is a novel adaptor-like modulator of the mitochondrial AAA+ protease CLPXP

Strack, P., Brodie, E., Zhan, H., Schuenemann, V., Saiyed, T., Zeth, K., Truscott, K., Dougan, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: cross-linking

Macromolecule Content

• Total Structure Weight: 34.46 kDa 
• Atom Count: 1,975 
• Modelled Residue Count: 240 
• Deposited Residue Count: 293 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymerase delta-interacting protein 2	A	293	Homo sapiens	Mutation(s): 0  Gene Names: POLDIP2, PDIP38, POLD4, HSPC017
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2S7 (Homo sapiens) Explore Q9Y2S7  Go to UniProtKB:  Q9Y2S7
PHAROS:  Q9Y2S7 GTEx:  ENSG00000004142

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PT	B [auth A], C [auth A]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.39 Å
• R-Value Free: 0.287 
• R-Value Work: 0.247 
• R-Value Observed: 0.249 
• Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.095	α = 90
b = 120.095	β = 90
c = 48.586	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-07-14 
Deposition Author(s): Zeth, K., Dougan, D.

Revision History  

• Version 1.0: 2021-07-14
  Type: Initial release
  
• Version 1.1: 2024-06-19
  Changes: Data collection, Database references