6ZLX | pdb_00006zlx

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.39 Å
R-Value Free:
0.287 (Depositor), 0.296 (DCC)
R-Value Work:
0.247 (Depositor), 0.260 (DCC)
R-Value Observed:
0.249 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 6ZLX

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
GTEx: ENSG00000004142
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y2S7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PT Query on PT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.39 Å
R-Value Free: 0.287 (Depositor), 0.296 (DCC)
R-Value Work: 0.247 (Depositor), 0.260 (DCC)
R-Value Observed: 0.249 (Depositor)

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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2021-07-14

Deposition Author(s):

Revision History (Full details and data files)

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

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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.