9M4N | pdb_00009m4n

Structure of AtCDC48

• PDB DOI: https://doi.org/10.2210/pdb9M4N/pdb

• Classification: PLANT PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2025-03-04 Released: 2025-10-29 
• Deposition Author(s): Sandholu, A.S., Zhang, J., Brandon, Z.H., Hameed, U.F.S., Arold, S.T.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free: 
  0.384 (Depositor), 0.371 (DCC) 
• R-Value Work: 
  0.346 (Depositor), 0.346 (DCC) 
• R-Value Observed: 
  0.348 (Depositor) 

Starting Model: in silico

Literature

Structure of AtCDC48 N-domain

Sandholu, A.S., Zhang, J., Brandon, Z.H., Hameed, U.F.S., Arold, S.T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C6  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 87.57 kDa 
• Atom Count: 5,203 
• Modeled Residue Count: 659 
• Deposited Residue Count: 784 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division control protein 48 homolog A	A	784	Arabidopsis thaliana	Mutation(s): 0  Gene Names: CDC48A, CDC48, At3g09840, F8A24.11
UniProt
Find proteins for P54609 (Arabidopsis thaliana) Explore P54609  Go to UniProtKB:  P54609

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	B [auth A], C [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.45 Å
• R-Value Free:  0.384 (Depositor), 0.371 (DCC) 
• R-Value Work:  0.346 (Depositor), 0.346 (DCC) 
• R-Value Observed: 0.348 (Depositor) 

Space Group: P 6 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.467	α = 90
b = 144.467	β = 90
c = 162.963	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-29 
Deposition Author(s): Sandholu, A.S., Zhang, J., Brandon, Z.H., Hameed, U.F.S., Arold, S.T.

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Funding Organization	Location	Grant Number
Other private	Saudi Arabia	URF/1/4039-01-01
Other private	Saudi Arabia	URF/1/4080-01-01

Revision History  

• Version 1.0: 2025-10-29
  Type: Initial release