4BRF

Legionella pneumophila NTPDase1 crystal form II (closed) in complex with a distorted orthomolybdate ion and AMP

Structural Biology Knowledgebase: 4BRF SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.184
  • R-Value Work: 0.125

Literature

Macromolecules
Sequence Display for 4BRF

Classification: HYDROLASE

Total Structure Weight: 85657.48

Macromolecule Entities
Molecule Chains Length Organism Details
ECTONUCLEOSIDE TRIPHOSPHATE DIPHOSPHOHYDROLASE I A, B 368 Legionella pneumophila EC#: 3.6.1.5 IUBMB
Fragment: RESIDUES 35-393
Mutation: E137D, A149V
Gene Name(s): lpg1905
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 9 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
M27
Query on M27

A bis(mu2-oxo)-octaoxo-dimolybdenum (VI)
dimolybdate [Mo(VI)2O10]8- (Synonym)
Mo2 O10
OMHJAEGSJTZMPB-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
AMP
Query on AMP

B ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MES
Query on MES

A, B 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MOO
Query on MOO

A, B MOLYBDATE ION
MOLYBDATE (Synonym)
Mo O4
MEFBJEMVZONFCJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.184
  • R-Value Work: 0.125
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 62.14 α = 90.00
b = 85.97 β = 106.14
c = 71.89 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-06-04
  • Released Date: 2013-07-17
  • Deposition author(s): Zebisch, M., Schaefer, P., Lauble, P., Straeter, N.

Revision History

  • 2014-05-28
    Type: Linkage | Details: CONECT, LINK
  • 2014-05-28
    Type: Non-polymer description | Details: HETSYN, REMARK 620, FORMUL, HETNAM
  • 2014-05-28
    Type: Other | Details: ANISOU, MASTER, REMARK 610
  • 2014-05-28
    Type: Atom nomenclature | Details: ATOM, HETATM
  • 2013-12-25
    Type: Function and keywords | Details: KEYWDS
  • 2013-08-28
    Type: Citation | Details: JRNL