9KCQ | pdb_00009kcq

Crystal structure of an ankyrin protein in complex with G-quadruplex

• PDB DOI: https://doi.org/10.2210/pdb9KCQ/pdb
• NAKB: 9KCQ

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


• Deposited: 2024-11-02 Released: 2025-11-05 
• Deposition Author(s): Ngo, K.H., Heddi, B., Winnerdy, F.R., Phan, A.T.
• Funding Organization(s): National Research Foundation (NRF, Singapore), Ministry of Education (MoE, Singapore)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free: 
  0.200 (Depositor), 0.198 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Models: experimental

Literature

X-ray structure of a G-quadruplex-ankyrin complex

Ngo, K.H., Heddi, B., Winnerdy, F.R., Phan, A.T.

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

Macromolecule Content 

• Total Structure Weight: 25.4 kDa 
• Atom Count: 1,961 
• Modeled Residue Count: 179 
• Deposited Residue Count: 191 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ankyrin	A	169	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')	B	22	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	D [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ACY	C [auth A]	ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N
NA	E [auth B], F [auth B], G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.77 Å
• R-Value Free:  0.200 (Depositor), 0.198 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.957	α = 90
b = 67.747	β = 90
c = 70.737	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
autoPROC	data reduction
autoPROC	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-05 
Deposition Author(s): Ngo, K.H., Heddi, B., Winnerdy, F.R., Phan, A.T.

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Funding Organization	Location	Grant Number
National Research Foundation (NRF, Singapore)	Singapore	NRF-NRFI2017-09
Ministry of Education (MoE, Singapore)	Singapore	MOE2018-T2-2-029

Revision History  

• Version 1.0: 2025-11-05
  Type: Initial release