8ZR0 | pdb_00008zr0

Crystal structure of Skd3 in complex with AMPPNP

• PDB DOI: https://doi.org/10.2210/pdb8ZR0/pdb

• Classification: CHAPERONE
• Organism(s): Danio rerio
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-06-03 Released: 2025-06-11 
• Deposition Author(s): Lee, S., Lee, C.
• Funding Organization(s): National Research Foundation (NRF, Korea)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.255 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: in silico

Literature

Crystal structure of Skd3 in complex with AMPPNP

Lee, S., Lee, C.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 61.45 kDa 
• Atom Count: 3,892 
• Modeled Residue Count: 480 
• Deposited Residue Count: 536 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Caseinolytic peptidase B protein homolog	A	536	Danio rerio	Mutation(s): 0  Gene Names: clpb
UniProt
Find proteins for A0A8M3AT32 (Danio rerio) Explore A0A8M3AT32  Go to UniProtKB:  A0A8M3AT32

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ANP (Subject of Investigation/LOI)	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.255 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.699	α = 90
b = 119.699	β = 90
c = 89.98	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-06-11 
Deposition Author(s): Lee, S., Lee, C.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2021M3A9G8022417
National Research Foundation (NRF, Korea)	Korea, Republic Of	NRF-2021R1A2C2009550

Revision History  

• Version 1.0: 2025-06-11
  Type: Initial release