4KA7

Structure of Organellar OligoPeptidase (E572Q) in complex with an endogenous substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Organellar oligopeptidase (OOP) provides a complementary pathway for targeting peptide degradation in mitochondria and chloroplasts.

Kmiec, B.Teixeira, P.F.Berntsson, R.P.Murcha, M.W.Branca, R.M.Radomiljac, J.D.Regberg, J.Svensson, L.M.Bakali, A.Langel, U.Lehtio, J.Whelan, J.Stenmark, P.Glaser, E.

(2013) Proc. Natl. Acad. Sci. U.S.A. 110: E3761-E3769


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Oligopeptidase A
A
714Arabidopsis thalianaMutation(s): 1 
Gene Names: OOP (TOP1)
EC: 3.4.24.70
Find proteins for Q94AM1 (Arabidopsis thaliana)
Go to UniProtKB:  Q94AM1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
short endogenous peptide substrate
C
4N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.466α = 90.00
b = 100.771β = 90.00
c = 132.484γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
REFMACrefinement
XSCALEdata scaling
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-18
    Type: Initial release
  • Version 1.1: 2018-05-16
    Type: Data collection, Refinement description, Source and taxonomy
  • Version 1.2: 2018-10-17
    Type: Data collection, Database references