5ULP

Structure of the NS5 methyltransferase from Zika bound to MS2042


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Development of a S-adenosylmethionine analog that intrudes the RNA-cap binding site of Zika methyltransferase.

Jain, R.Butler, K.V.Coloma, J.Jin, J.Aggarwal, A.K.

(2017) Sci Rep 7: 1632-1632

  • DOI: 10.1038/s41598-017-01756-7

  • PubMed Abstract: 
  • The Zika virus (ZIKV) has emerged as a major health hazard. We present here a high resolution structure (1.55 Å) of ZIKV NS5 methyltransferase bound to a novel S-adenosylmethionine (SAM) analog in which a 4-fluorophenyl moiety substitutes for the met ...

    The Zika virus (ZIKV) has emerged as a major health hazard. We present here a high resolution structure (1.55 Å) of ZIKV NS5 methyltransferase bound to a novel S-adenosylmethionine (SAM) analog in which a 4-fluorophenyl moiety substitutes for the methyl group. We show that the 4-fluorophenyl moiety extends into a portion of the RNA binding tunnel that typically contains the adenosine 2'OH of the RNA-cap moiety. Together, the new SAM analog and the high-resolution crystal structure are a step towards the development of antivirals against ZIKV and other flaviviruses.


    Organizational Affiliation

    Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, New York, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MRNA cap 0-1 NS5-type methyltransferase
A, B
268Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013)Mutation(s): 0 
Find proteins for A0A024B7W1 (Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013))
Go to UniProtKB:  A0A024B7W1
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
URE
Query on URE

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A, B
UREA
C H4 N2 O
XSQUKJJJFZCRTK-UHFFFAOYSA-N
 Ligand Interaction
IPA
Query on IPA

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A
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
KB1
Query on KB1

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Download CCD File 
A, B
5'-{[(3S)-3-amino-3-carboxypropyl][(4-fluorophenyl)methyl]amino}-5'-deoxyadenosine
C21 H26 F N7 O5
UBYUMSGWGXUICY-SWQDORGXSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KB1Kd: 24300 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 38.989α = 90.00
b = 111.231β = 93.87
c = 77.400γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
Auto-Rickshawphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2017-05-31
    Type: Database references