6DLR

PRPP Riboswitch bound to PRPP, iridium-hexamine soaked structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.656 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

ykkC riboswitches employ an add-on helix to adjust specificity for polyanionic ligands.

Peselis, A.Serganov, A.

(2018) Nat. Chem. Biol. 14: 887-894


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
PRPP RiboswitchA107Syntrophothermus lipocalidus DSM 12680
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
PRP
Query on PRP

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A
ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID
C5 H13 O14 P3
PQGCEDQWHSBAJP-TXICZTDVSA-N
 Ligand Interaction
MG
Query on MG

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

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A
IRIDIUM HEXAMMINE ION
H18 Ir N6
CGMAOQLDNKCXGK-RIUFHJFFAL
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CCC
Query on CCC
A
RNA LINKINGC9 H13 N3 O10 P2C
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.656 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 83.520α = 90.00
b = 92.677β = 121.21
c = 74.487γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01GM112940
National Institutes of Health/National Institute of General Medical SciencesUnited StatesF31GM119357
National Institutes of Health/National Institute of General Medical SciencesUnited StatesT32GM88118

Revision History 

  • Version 1.0: 2018-11-14
    Type: Initial release