2C95 | pdb_00002c95

Structure of adenylate kinase 1 in complex with P1,P4-di(adenosine) tetraphosphate

• PDB DOI: https://doi.org/10.2210/pdb2C95/pdb

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


• Deposited: 2005-12-09 Released: 2007-02-20 
• Deposition Author(s): Bunkoczi, G., Filippakopoulos, P., Jansson, A., Longman, E., von Delft, F., Edwards, A., Arrowsmith, C., Sundstrom, M., Knapp, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 
  0.228 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Structure of Adenylate Kinase 1 in Complex with P1, P4-Di(Adenosine)Tetraphosphate

Bunkoczi, G., Filippakopoulos, P., Jansson, A., Longman, E., von Delft, F., Edwards, A., Arrowsmith, C., Sundstrom, M., Weigelt, J., Knapp, S.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 45.55 kDa 
• Atom Count: 3,531 
• Modeled Residue Count: 389 
• Deposited Residue Count: 392 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADENYLATE KINASE 1	A, B	196	Homo sapiens	Mutation(s): 0  EC: 2.7.4.3 (PDB Primary Data), 2.7.4.4 (UniProt), 2.7.4.6 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00568 (Homo sapiens) Explore P00568  Go to UniProtKB:  P00568
PHAROS:  P00568 GTEx:  ENSG00000106992

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B4P	C [auth A], E [auth B]	BIS(ADENOSINE)-5'-TETRAPHOSPHATE C20 H28 N10 O19 P4 YOAHKNVSNCMZGQ-XPWFQUROSA-N
MLI	D [auth A], F [auth B]	MALONATE ION C3 H2 O4 OFOBLEOULBTSOW-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free:  0.228 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.535	α = 90
b = 69.998	β = 90
c = 88.558	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-02-20 
Deposition Author(s): Bunkoczi, G., Filippakopoulos, P., Jansson, A., Longman, E., von Delft, F., Edwards, A., Arrowsmith, C., Sundstrom, M., Knapp, S.

Revision History  

• Version 1.0: 2007-02-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Refinement description, Version format compliance
• Version 1.2: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.3: 2018-04-04
  Changes: Data collection
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description