5AK7

Structure of wt Porphyromonas gingivalis peptidylarginine deiminase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.128 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of Porphyromonas Gingivalis Peptidylarginine Deiminase: Implications for Autoimmunity in Rheumatoid Arthritis.

Montgomery, A.B.Kopec, J.Shrestha, L.Thezenas, M.L.Burgess-Brown, N.A.Fischer, R.Yue, W.W.Venables, P.J.

(2016) Ann.Rheum.Dis. 75: 1255

  • DOI: 10.1136/annrheumdis-2015-207656
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Periodontitis (PD) is a known risk factor for rheumatoid arthritis (RA) and there is increasing evidence that the link between the two diseases is due to citrullination by the unique bacterial peptidylarginine deiminase (PAD) enzyme expressed by peri ...

    Periodontitis (PD) is a known risk factor for rheumatoid arthritis (RA) and there is increasing evidence that the link between the two diseases is due to citrullination by the unique bacterial peptidylarginine deiminase (PAD) enzyme expressed by periodontal pathogen Pophyromonas gingivalis (PPAD). However, the precise mechanism by which PPAD could generate potentially immunogenic peptides has remained controversial due to lack of information about the structural and catalytic mechanisms of the enzyme.


    Organizational Affiliation

    Kennedy institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PEPTIDYLARGININE DEIMINASE
A
438Porphyromonas gingivalis (strain ATCC BAA-308 / W83)Mutation(s): 0 
EC: 3.5.3.-
Find proteins for Q9RQJ2 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
Go to UniProtKB:  Q9RQJ2
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ALA
Query on ALA

Download SDF File 
Download CCD File 
A
ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-REOHCLBHSA-N
 Ligand Interaction
ARG
Query on ARG

Download SDF File 
Download CCD File 
A
ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.128 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 101.860α = 90.00
b = 84.660β = 92.50
c = 55.660γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
Rosettaphasing
REFMACrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 1.1: 2015-08-05
    Type: Database references
  • Version 1.2: 2015-08-19
    Type: Structure summary
  • Version 1.3: 2016-05-25
    Type: Database references