6FZ0

Crystal structure of the metY SAM V riboswitch


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.499 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structure and ligand binding of the SAM-V riboswitch.

Huang, L.Lilley, D.M.

(2018) Nucleic Acids Res. --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
metY SAM V (53-MER)A53Candidatus Pelagibacter ubique HTCC1062
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
SAM
Query on SAM

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A
S-ADENOSYLMETHIONINE
C15 H22 N6 O5 S
MEFKEPWMEQBLKI-FCKMPRQPSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CBV
Query on CBV
A
RNA LINKINGC9 H13 Br N3 O8 PC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.499 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.231 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 87.828α = 90.00
b = 87.828β = 90.00
c = 62.670γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
PHENIXphasing
xia2data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomA18604

Revision History 

  • Version 1.0: 2018-07-04
    Type: Initial release