3AKD

Crystal structure of CMP kinase in complex with CDP from Thermus thermophilus HB8

• PDB DOI: https://doi.org/10.2210/pdb3AKD/pdb

• Classification: TRANSFERASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-07-12 Released: 2011-07-06 
• Deposition Author(s): Mega, R., Nakagawa, N., Kuramitsu, S., Masui, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.236 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of the tertiary complex of CMP kinase with a phosphoryl group acceptor and a donor from Thermus thermophilus HB8

Mega, R., Nakagawa, N., Kuramitsu, S., Masui, R.

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)

Macromolecule Content

• Total Structure Weight: 22.99 kDa 
• Atom Count: 1,668 
• Modelled Residue Count: 202 
• Deposited Residue Count: 208 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytidylate kinase	A	208	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: TTHA0458 EC: 2.7.4.14 (PDB Primary Data), 2.7.4.25 (UniProt)
UniProt
Find proteins for Q5SL35 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SL35  Go to UniProtKB:  Q5SL35

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CDP	B [auth A]	CYTIDINE-5'-DIPHOSPHATE C9 H15 N3 O11 P2 ZWIADYZPOWUWEW-XVFCMESISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.236 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.929	α = 90
b = 61.929	β = 90
c = 111.099	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
ARP/wARP	model building
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-06 
Deposition Author(s): Mega, R., Nakagawa, N., Kuramitsu, S., Masui, R.

Revision History  

• Version 1.0: 2011-07-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description