9LDC | pdb_00009ldc

The structure of TkoKptA/DNA/ADPR complex-B*

• PDB DOI: https://doi.org/10.2210/pdb9LDC/pdb
• NAKB: 9LDC

• Classification: TRANSFERASE/DNA
• Organism(s): Thermococcus kodakarensis KOD1, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• 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: 1.97 Å
• R-Value Free: 
  0.242 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: in silico

Literature

The structure of TkoKptA/DNA/ADPR complex-B*

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: 24.89 kDa 
• Atom Count: 1,612 
• 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): 0  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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
A1EJT	A	L-PEPTIDE LINKING	C21 H35 N7 O15 P2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.242 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.256	α = 90
b = 84.256	β = 90
c = 66.578	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