5K77

Dbr1 in complex with 7-mer branched RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Metal dependence and branched RNA cocrystal structures of the RNA lariat debranching enzyme Dbr1.

Clark, N.E.Katolik, A.Roberts, K.M.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. U.S.A. 113: 14727-14732


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'-UAA(-2'GU)CA-3'V,W,X,Y,Z5Saccharomyces cerevisiae
Entity ID: 3
MoleculeChainsLengthOrganism
brnch 2 of branched RNA 5'-UAA(-2'GU)CA-3'v,w,x,y,z2Saccharomyces cerevisiae
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

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

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Download CCD File 
A, B, C, D, E
HYDROXIDE ION
H O
XLYOFNOQVPJJNP-UHFFFAOYSA-M
 Ligand Interaction
FE2
Query on FE2

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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: 2.17 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 73.151α = 90.00
b = 141.892β = 90.00
c = 212.511γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
PHENIXrefinement

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: 2018-04-18
    Type: Data collection, Database references