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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free:
0.242 (Depositor), 0.247 (DCC)
R-Value Work:
0.194 (Depositor)
R-Value Observed:
0.197 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 9KH2

This is version 1.0 of the entry. See complete history.

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.

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

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HC78
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 2
DNA (5'-D(CPAPAPTPGPTPAPTPGPGPCPC)-3')	C, F	12	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism	Image
Entity ID: 3
DNA (5'-D(GPGPCPCPAPTPAPCPAPTPTPG)-3')	D, E	12	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] J [auth B] K [auth B] G [auth A], H [auth A], I [auth A], J [auth B], K [auth B], L [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.59 Å
R-Value Free: 0.242 (Depositor), 0.247 (DCC)
R-Value Work: 0.194 (Depositor)
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

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-11-26

Deposition Author(s):

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

Revision History (Full details and data files)

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

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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.