5LDB

Crystal Structure of Polyphosphate Kinase from Meiothermus ruber bound to ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 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
287Meiothermus ruber H328Mutation(s): 0 
Find proteins for A0A0S7ASE9 (Meiothermus ruber H328)
Go to UniProtKB:  A0A0S7ASE9
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ADP
Query on ADP

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Download CCD File 
A, B, C, D
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.177 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 165.619α = 90.00
b = 165.619β = 90.00
c = 95.150γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
AutoPROCdata collection
Aimlessdata scaling
BUSTER-TNTrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-06-21
    Type: Initial release
  • Version 1.1: 2018-03-21
    Type: Database references
  • Version 1.2: 2018-04-11
    Type: Data collection, Database references