5O6M

Structure of Polyphosphate Kinase from Meiothermus ruber N121D bound to ATP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Substrate recognition and mechanism revealed by ligand-bound polyphosphate kinase 2 structures.

Parnell, A.E.Mordhorst, S.Kemper, F.Giurrandino, M.Prince, J.P.Schwarzer, N.J.Hofer, A.Wohlwend, D.Jessen, H.J.Gerhardt, S.Einsle, O.Oyston, P.C.F.Andexer, J.N.Roach, P.L.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: 3350-3355


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Polyphosphate:AMP phosphotransferase
A, B, C, D
267Meiothermus ruber (strain ATCC 35948 / DSM 1279 / VKM B-1258 / 21)Mutation(s): 1 
EC: 2.7.4.-, 2.7.4.1
Find proteins for M9XB82 (Meiothermus ruber (strain ATCC 35948 / DSM 1279 / VKM B-1258 / 21))
Go to UniProtKB:  M9XB82
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download SDF File 
Download CCD File 
A, B, C, D
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.195 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 164.620α = 90.00
b = 164.620β = 90.00
c = 95.125γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHENIXphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2018-04-11
    Type: Data collection, Database references