4FFS | pdb_00004ffs

Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Helicobacter pylori with butyl-thio-DADMe-Immucillin-A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.192 (Depositor), 0.200 (DCC) 
  • R-Value Work: 
    0.161 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.163 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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Literature

A Picomolar Transition State Analogue Inhibitor of MTAN as a Specific Antibiotic for Helicobacter pylori.

Wang, S.Haapalainen, A.M.Yan, F.Du, Q.Tyler, P.C.Evans, G.B.Rinaldo-Matthis, A.Brown, R.L.Norris, G.E.Almo, S.C.Schramm, V.L.

(2012) Biochemistry 51: 6892-6894

  • DOI: https://doi.org/10.1021/bi3009664
  • Primary Citation of Related Structures:  
    4FFS

  • PubMed Abstract: 

    Campylobacter and Helicobacter species express a 6-amino-6-deoxyfutalosine N-ribosylhydrolase (HpMTAN) proposed to function in menaquinone synthesis. BuT-DADMe-ImmA is a 36 pM transition state analogue of HpMTAN, and the crystal structure of the enzyme-inhibitor complex reveals the mechanism of inhibition. BuT-DADMe-ImmA has a MIC(90) value of <8 ng/mL for Helicobacter pylori growth but does not cause growth arrest in other common clinical pathogens, thus demonstrating potential as an H. pylori-specific antibiotic.


  • Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
MTA/SAH nucleosidase239Helicobacter pylori J99Mutation(s): 0 
Gene Names: jhp_0082mtnmtnNPfs
EC: 3.2.2.9 (PDB Primary Data), 3.2.2.30 (UniProt)
UniProt
Find proteins for Q9ZMY2 (Helicobacter pylori (strain J99 / ATCC 700824))
Explore Q9ZMY2 
Go to UniProtKB:  Q9ZMY2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZMY2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BIG
Query on BIG

Download Ideal Coordinates CCD File 
B [auth A](3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl]-4-[(butylsulfanyl)methyl]pyrrolidin-3-ol
C16 H25 N5 O S
LTSUEVPGSXUJHT-OLZOCXBDSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
BIG BindingDB:  4FFS Kd: 50 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.192 (Depositor), 0.200 (DCC) 
  • R-Value Work:  0.161 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.163 (Depositor) 
Space Group: I 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157.732α = 90
b = 157.732β = 90
c = 157.732γ = 90
Software Package:
Software NamePurpose
XDisplayFdata collection
MOLREPphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted BIGClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-09-26
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations