4BVP

Legionella pneumophila NTPDase1 crystal form II (closed) in complex with heptamolybdate and octamolybdate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.127 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structures of Legionella Pneumophila Ntpdase1 in Complex with Polyoxometallates.

Zebisch, M.Krauss, M.Schafer, P.Strater, N.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1147

  • DOI: https://doi.org/10.1107/S1399004714001916
  • Primary Citation of Related Structures:  
    4BVO, 4BVP

  • PubMed Abstract: 

    Nucleoside triphosphate diphosphohydrolases (NTPDases) are secreted or membrane-bound ectonucleotidases that hydrolyze the anhydride bonds of nucleoside triphosphates and nucleoside diphosphates. Mammalian cell-surface NTPDase enzymes are inhibited by various polyoxometallates. Here, the structures of NTPDase1 from the bacterium Legionella pneumophila (LpNTPDase1) in complex with the dodecatungstate POM-1, decavanadate and octamolybdate/heptamolybdate are described. The metal clusters are bound at different sites but always in a highly ordered fashion via electrostatic interactions and hydrogen bonds. For octamolybdate, covalent interactions after oxygen ligand exchange by a serine and histidine side chain are also observed. The potential inhibitory mechanism and the use of the metal clusters as phasing tools for new NTPDase structures are discussed. The binding mode of a tartrate ion at the catalytic centre suggests novel strategies for the structure-based design of NTPDase inhibitors, and the observation of the enzyme in an intermediate open state contributes to our understanding of NTPDase enzyme dynamics.


  • Organizational Affiliation

    Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, University of Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I
A, B
368Legionella pneumophilaMutation(s): 0 
UniProt
Find proteins for Q5ZUA2 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZUA2 
Go to UniProtKB:  Q5ZUA2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZUA2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8M0
Query on 8M0

Download Ideal Coordinates CCD File 
R [auth A],
U [auth B]
bis(mu4-oxo)-tetrakis(mu3-oxo)-hexakis(mu2-oxo)-hexadecaoxo-octamolybdenum (VI)
Mo8 O28
GSOSAILZTJNYOK-UHFFFAOYSA-N
MO7
Query on MO7

Download Ideal Coordinates CCD File 
HA [auth B],
P [auth A]
bis(mu4-oxo)-bis(mu3-oxo)-octakis(mu2-oxo)-dodecaoxo-heptamolybdenum (VI)
Mo7 O24
CFQDGBTUZUJXQE-UHFFFAOYSA-N
6LL
Query on 6LL

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EA [auth B],
M [auth A]
TETRAKIS-(MU-OXO)-DECA-OXO-TRIMOLYBDENUM
Mo3 O14
VGYKEVLINQLXTN-UHFFFAOYSA-N
M27
Query on M27

Download Ideal Coordinates CCD File 
AA [auth B],
CA [auth B],
I [auth A],
K [auth A]
bis(mu2-oxo)-octaoxo-dimolybdenum (VI)
Mo2 O10
OMHJAEGSJTZMPB-UHFFFAOYSA-N
MES
Query on MES

Download Ideal Coordinates CCD File 
F [auth A],
X [auth B]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
MOO
Query on MOO

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D [auth A],
V [auth B]
MOLYBDATE ION
Mo O4
MEFBJEMVZONFCJ-UHFFFAOYSA-N
GOL
Query on GOL

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BA [auth B]
DA [auth B]
FA [auth B]
H [auth A]
IA [auth B]
BA [auth B],
DA [auth B],
FA [auth B],
H [auth A],
IA [auth B],
N [auth A],
Z [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

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GA [auth B],
J [auth A],
L [auth A],
O [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

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Q [auth A],
T [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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E [auth A],
G [auth A],
S [auth A],
W [auth B],
Y [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.49 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.127 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.564α = 90
b = 85.436β = 103.94
c = 71.779γ = 90
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-12
    Type: Initial release
  • Version 1.1: 2014-04-09
    Changes: Database references
  • Version 1.2: 2014-04-16
    Changes: Database references
  • Version 1.3: 2014-12-17
    Changes: Atomic model, Derived calculations, Non-polymer description, Other
  • Version 1.4: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary