1RKB

The structure of adrenal gland protein AD-004


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The crystal structure of human adenylate kinase 6: An adenylate kinase localized to the cell nucleus

Ren, H.Wang, L.Bennett, M.Liang, Y.Zheng, X.Lu, F.Li, L.Nan, J.Luo, M.Eriksson, S.Zhang, C.Su, X.D.

(2005) Proc.Natl.Acad.Sci.Usa 102: 303-308

  • DOI: 10.1073/pnas.0407459102

  • PubMed Abstract: 
  • Adenylate kinases (AKs) play important roles in nucleotide metabolism in all organisms and in cellular energetics by means of phosphotransfer networks in eukaryotes. The crystal structure of a human AK named AK6 was determined by in-house sulfur sing ...

    Adenylate kinases (AKs) play important roles in nucleotide metabolism in all organisms and in cellular energetics by means of phosphotransfer networks in eukaryotes. The crystal structure of a human AK named AK6 was determined by in-house sulfur single-wavelength anomalous dispersion phasing methods and refined to 2.0-A resolution with a free R factor of 21.8%. Sequence analyses revealed that human AK6 belongs to a distinct subfamily of AKs present in all eukaryotic organisms sequenced so far. Enzymatic assays show that human AK6 has properties similar with other AKs, particularly with AK5. Fluorescence microscopy showed that human AK6 is localized predominantly to the nucleus of HeLa cells. The identification of a nuclear-localized AK sheds light on nucleotide metabolism in the nucleus and the energetic communication between mitochondria and nucleus by means of phosphotransfer networks.


    Organizational Affiliation

    National Laboratory of Protein Engineering and Plant Genetic Engineering and Department of Biochemistry and Molecular Biology, College of Life Sciences, Peking University, Beijing 100871, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein AD-004
A
173Homo sapiensMutation(s): 0 
Gene Names: AK6 (CINAP)
EC: 2.7.4.3
Find proteins for Q9Y3D8 (Homo sapiens)
Go to Gene View: AK6
Go to UniProtKB:  Q9Y3D8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LI
Query on LI

Download SDF File 
Download CCD File 
A
LITHIUM ION
Li
HBBGRARXTFLTSG-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.203 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 99.555α = 90.00
b = 99.555β = 90.00
c = 57.191γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
PROTEUM PLUSdata scaling
RESOLVEphasing
PROTEUM PLUSdata reduction
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-01-11
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance