2BBW

Crystal structure of human adenylate kinase 4 (AK4) in complex with diguanosine pentaphosphate

• PDB DOI: https://doi.org/10.2210/pdb2BBW/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-10-17 Released: 2005-12-06 
• Deposition Author(s): Filippakopoulos, P., Turnbull, A.P., Fedorov, O., Weigelt, J., Bunkoczi, G., Ugochukwu, E., Debreczeni, J., Niesen, F., von Delft, F., Edwards, A., Arrowsmith, C., Sundstrom, M., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.249 
• R-Value Work: 0.180 
• R-Value Observed: 0.183 

Starting Model: experimental

Literature

Crystal structure of human adenylate kinase 4 (AK4) in complex with diguanosine pentaphosphate

Filippakopoulos, P., Turnbull, A.P., Fedorov, O., Weigelt, J., Bunkoczi, G., Ugochukwu, E., Debreczeni, J., Niesen, F., von Delft, F., Edwards, A., Arrowsmith, C., Sundstrom, M., Knapp, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 57.85 kDa 
• Atom Count: 3,720 
• Modelled Residue Count: 440 
• Deposited Residue Count: 492 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
adenylate kinase 4, AK4	A, B	246	Homo sapiens	Mutation(s): 0  Gene Names: AK4 EC: 2.7.4.3
UniProt & NIH Common Fund Data Resources
Find proteins for P27144 (Homo sapiens) Explore P27144  Go to UniProtKB:  P27144
GTEx:  ENSG00000162433

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GP5	C [auth A], D [auth B]	DIGUANOSINE-PENTAPHOSPHATE C20 H29 N10 O24 P5 RELSGTOCAPVUGP-DTFXMBEISA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.249 
• R-Value Work: 0.180 
• R-Value Observed: 0.183 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.836	α = 90
b = 66.375	β = 91.5
c = 77.38	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-06 
Deposition Author(s): Filippakopoulos, P., Turnbull, A.P., Fedorov, O., Weigelt, J., Bunkoczi, G., Ugochukwu, E., Debreczeni, J., Niesen, F., von Delft, F., Edwards, A., Arrowsmith, C., Sundstrom, M., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2005-12-06
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description