9LDA | pdb_00009lda

The complex structure of K63A/5'-p-ADPR-DNA

• PDB DOI: https://doi.org/10.2210/pdb9LDA/pdb

• Classification: TRANSFERASE/DNA
• Organism(s): Thermococcus kodakarensis KOD1, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-01-05 Released: 2025-11-12 
• Deposition Author(s): Cao, C.L., Yang, J., Zhang, W.Z., Gan, J.H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 
  0.249 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Starting Model: in silico

Literature

The complex structure of K63A/5'-p-ADPR-DNA

Cao, C.L., Yang, J., Zhang, W.Z., Gan, J.H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 24.73 kDa 
• Atom Count: 1,527 
• Modeled Residue Count: 181 
• Deposited Residue Count: 190 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable RNA 2'-phosphotransferase	A	180	Thermococcus kodakarensis KOD1	Mutation(s): 1  Gene Names: kptA, TK0302 EC: 2.7.1
UniProt
Find proteins for Q5JFX3 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JFX3  Go to UniProtKB:  Q5JFX3

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')	B	10	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EJJ (Subject of Investigation/LOI)	E [auth B]	[[(2~{R},3~{S},4~{R},5~{S})-5-(4-azanyl-5~{H}-pyrrolo[3,2-d]pyrimidin-7-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{S})-3,4,5-tris(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate C16 H24 N4 O14 P2 OTAOKDBQHDLBAB-RXFQNIHHSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
IMD	C [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free:  0.249 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.057	α = 90
b = 85.057	β = 90
c = 67.178	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Cao, C.L., Yang, J., Zhang, W.Z., Gan, J.H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release