9KH2 | pdb_00009kh2

Crystal structure of the first three zinc finger domains of ZBTB20 in complex with DNA

• PDB DOI: https://doi.org/10.2210/pdb9KH2/pdb
• NAKB: 9KH2

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-11-09 Released: 2025-11-26 
• Deposition Author(s): Chen, X., Luo, Z., Song, Y., Xu, S., Wu, J., Duan, B.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 
  0.242 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Literature

Crystal structure of the first three zinc finger domains of ZBTB20 in complex with DNA

Chen, X., Luo, Z., Wu, J., Duan, B.

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: isothermal titration calorimetry

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 35.01 kDa 
• Atom Count: 2,394 
• Modeled Residue Count: 216 
• Deposited Residue Count: 216 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc finger and BTB domain-containing protein 20	A, B	84	Homo sapiens	Mutation(s): 0  Gene Names: ZBTB20, DPZF, ZNF288
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HC78 (Homo sapiens) Explore Q9HC78  Go to UniProtKB:  Q9HC78
PHAROS:  Q9HC78 GTEx:  ENSG00000181722

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*AP*AP*TP*GP*TP*AP*TP*GP*GP*CP*C)-3')	C, F	12	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*CP*CP*AP*TP*AP*CP*AP*TP*TP*G)-3')	D, E	12	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], L [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free:  0.242 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.676	α = 90
b = 147.788	β = 90
c = 143.016	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-26 
Deposition Author(s): Chen, X., Luo, Z., Song, Y., Xu, S., Wu, J., Duan, B.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	32100969

Revision History  

• Version 1.0: 2025-11-26
  Type: Initial release