5K78

Dbr1 in complex with 16-mer branched RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The RNA lariat debranching enzyme Dbr1: metal dependence and branched RNA co-crystal structures

Clark, N.E.Katolik, A.Roberts, K.Taylor, A.B.Holloway, S.P.Schuermann, J.P.Montemayor, E.J.Stevens, S.W.Fitzpatrick, P.F.Damha, M.J.Hart, P.J.

(2016) Proc.Natl.Acad.Sci.USA --: --


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA lariat debranching enzyme, putative
A, B, C, D, E
360Entamoeba histolyticaMutation(s): 1 
Find proteins for C4M1P9 (Entamoeba histolytica)
Go to UniProtKB:  C4M1P9
Entity ID: 2
MoleculeChainsLengthOrganism
branch 1 of branched RNA 5'-UACUAA(2'-GUAUGU)CAAGU-3'X,Y11Saccharomyces cerevisiae
Entity ID: 3
MoleculeChainsLengthOrganism
branch 2 of branched RNA 5'-UACUAA(2'-GUAUGU)CAAGU-3'x,y6Saccharomyces cerevisiae
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D, E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FE2
Query on FE2

Download SDF File 
Download CCD File 
A, B, C, D, E
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 73.893α = 90.00
b = 142.673β = 90.00
c = 215.131γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
Aimlessdata scaling
PHENIXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2016-12-14
    Type: Derived calculations
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence