4TKX

Structure of Protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.122 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of the lysine specific protease Kgp from Porphyromonas gingivalis, a target for improved oral health.

Gorman, M.A.Seers, C.A.Michell, B.J.Feil, S.C.Huq, N.L.Cross, K.J.Reynolds, E.C.Parker, M.W.

(2015) Protein Sci 24: 162-166

  • DOI: 10.1002/pro.2589
  • Primary Citation of Related Structures:  
    4TKX

  • PubMed Abstract: 
  • The oral pathogen Porphyromonas gingivalis is a keystone pathogen in the development of chronic periodontitis. Gingipains, the principle virulence factors of P. gingivalis are multidomain, cell-surface proteins containing a cysteine protease domain. The lysine specific gingipain, Kgp, is a critical virulence factor of P ...

    The oral pathogen Porphyromonas gingivalis is a keystone pathogen in the development of chronic periodontitis. Gingipains, the principle virulence factors of P. gingivalis are multidomain, cell-surface proteins containing a cysteine protease domain. The lysine specific gingipain, Kgp, is a critical virulence factor of P. gingivalis. We have determined the X-ray crystal structure of the lysine-specific protease domain of Kgp to 1.6 Å resolution. The structure provides insights into the mechanism of substrate specificity and catalysis.


    Organizational Affiliation

    ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, Victoria, 3065, Australia.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lys-gingipain W83A [auth L]452Porphyromonas gingivalisMutation(s): 0 
Gene Names: kgpprtKprtP
EC: 3.4.22.47
Find proteins for Q51817 (Porphyromonas gingivalis)
Explore Q51817 
Go to UniProtKB:  Q51817
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TCK
Query on TCK

Download Ideal Coordinates CCD File 
U [auth L]N-[(1S)-5-amino-1-(chloroacetyl)pentyl]-4-methylbenzenesulfonamide
C14 H21 Cl N2 O3 S
RDFCSSHDJSZMTQ-ZDUSSCGKSA-N
 Ligand Interaction
PB
Query on PB

Download Ideal Coordinates CCD File 
T [auth L]LEAD (II) ION
Pb
RVPVRDXYQKGNMQ-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth L], C [auth L], D [auth L], E [auth L]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
J [auth L] , K [auth L] , L , M [auth L] , N [auth L] , O [auth L] , P [auth L] , Q [auth L] , 
J [auth L],  K [auth L],  L,  M [auth L],  N [auth L],  O [auth L],  P [auth L],  Q [auth L],  R [auth L],  S [auth L]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
I [auth L]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
H [auth L]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth L], G [auth L]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 8
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000459 (TCK)
Query on PRD_000459
U [auth L]Tosyl-L-lysine chloromethyl ketonePeptide-like /  Inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.145 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.122 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.941α = 90
b = 116.941β = 90
c = 86.852γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
SHELXphasing
Cootmodel building
Aimlessdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-31
    Type: Initial release
  • Version 1.1: 2015-01-14
    Changes: Database references
  • Version 1.2: 2015-02-04
    Changes: Derived calculations
  • Version 1.3: 2015-04-08
    Changes: Non-polymer description
  • Version 1.4: 2017-09-27
    Changes: Advisory, Data collection, Derived calculations, Refinement description, Source and taxonomy