9LDG | pdb_00009ldg

The structure of TkoKptA/DNA/Appr>P complex-B

• PDB DOI: https://doi.org/10.2210/pdb9LDG/pdb
• NAKB: 9LDG

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


• Deposited: 2025-01-06 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: 2.40 Å
• R-Value Free: 
  0.290 (Depositor), 0.289 (DCC) 
• R-Value Work: 
  0.236 (Depositor), 0.237 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Starting Model: in silico

Literature

The structure of TkoKptA/DNA/Appr>P complex-B

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

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 49.56 kDa 
• Atom Count: 3,273 
• Modeled Residue Count: 373 
• Deposited Residue Count: 380 
• 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, B	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(*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')	C, D	10	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1EJE (Subject of Investigation/LOI)	E [auth A], G [auth B]	[[(3~{a}~{R},5~{R},6~{R},6~{a}~{R})-2,6-bis(oxidanyl)-2-oxidanylidene-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3,2]dioxaphosphol-5-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate C15 H22 N5 O16 P3 NPSPRYXPOGPCPM-KEOHHSTQSA-N
GOL	F [auth A], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.290 (Depositor), 0.289 (DCC) 
• R-Value Work:  0.236 (Depositor), 0.237 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.078	α = 90
b = 59.397	β = 94.04
c = 65.749	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
autoPROC	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