4TKX | pdb_00004tkx

Structure of Protease

PDB DOI: https://doi.org/10.2210/pdb4TKX/pdb

Classification: Hydrolase/Hydrolase Inhibitor
Organism(s): Porphyromonas gingivalis
Expression System: Porphyromonas gingivalis
Mutation(s): No

Deposited: 2014-05-28 Released: 2014-12-31
Deposition Author(s): Gorman, M.A., Parker, M.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.145 (Depositor), 0.150 (DCC)
R-Value Work:
0.120 (Depositor), 0.127 (DCC)
R-Value Observed:
0.122 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 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

PubMed: 25327141 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/pro.2589
Primary Citation 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. 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.

Macromolecule Content

Total Structure Weight: 51.59 kDa
Atom Count: 4,164
Modeled Residue Count: 452
Deposited Residue Count: 452
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lys-gingipain W83	A [auth L]	452	Porphyromonas gingivalis	Mutation(s): 0 Gene Names: kgp, prtK, prtP EC: 3.4.22.47
UniProt
Find proteins for Q51817 (Porphyromonas gingivalis) Explore Q51817 Go to UniProtKB: Q51817
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q51817
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TCK Query on TCK Download:Ideal Coordinates CCD File SDF format, chain U [auth L] MOL2 format, chain U [auth L] mmCIF format, chain U [auth L]	U [auth L]	N-[(1S)-5-amino-1-(chloroacetyl)pentyl]-4-methylbenzenesulfonamide C₁₄ H₂₁ Cl N₂ O₃ S RDFCSSHDJSZMTQ-ZDUSSCGKSA-N		Interactions Focus chain U [auth L] Interactions & Density Focus chain U [auth L]
PB Query on PB Download:Ideal Coordinates CCD File SDF format, chain T [auth L] MOL2 format, chain T [auth L] mmCIF format, chain T [auth L]	T [auth L]	LEAD (II) ION Pb RVPVRDXYQKGNMQ-UHFFFAOYSA-N		Interactions Focus chain T [auth L] Interactions & Density Focus chain T [auth L]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain B [auth L] SDF format, chain C [auth L] SDF format, chain D [auth L] SDF format, chain E [auth L] MOL2 format, chain B [auth L] MOL2 format, chain C [auth L] MOL2 format, chain D [auth L] MOL2 format, chain E [auth L] mmCIF format, chain B [auth L] mmCIF format, chain C [auth L] mmCIF format, chain D [auth L] mmCIF format, chain E [auth L]	B [auth L], C [auth L], D [auth L], E [auth L]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth L] Focus chain C [auth L] Focus chain D [auth L] Focus chain E [auth L] Interactions & Density Focus chain B [auth L] Focus chain C [auth L] Focus chain D [auth L] Focus chain E [auth L]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain J [auth L] SDF format, chain K [auth L] SDF format, chain L SDF format, chain M [auth L] SDF format, chain N [auth L] SDF format, chain O [auth L] SDF format, chain P [auth L] SDF format, chain Q [auth L] SDF format, chain R [auth L] SDF format, chain S [auth L] MOL2 format, chain J [auth L] MOL2 format, chain K [auth L] MOL2 format, chain L MOL2 format, chain M [auth L] MOL2 format, chain N [auth L] MOL2 format, chain O [auth L] MOL2 format, chain P [auth L] MOL2 format, chain Q [auth L] MOL2 format, chain R [auth L] MOL2 format, chain S [auth L] mmCIF format, chain J [auth L] mmCIF format, chain K [auth L] mmCIF format, chain L mmCIF format, chain M [auth L] mmCIF format, chain N [auth L] mmCIF format, chain O [auth L] mmCIF format, chain P [auth L] mmCIF format, chain Q [auth L] mmCIF format, chain R [auth L] mmCIF format, chain S [auth L]	J [auth L] K [auth L] L M [auth L] N [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		Interactions Focus chain J [auth L] Focus chain K [auth L] Focus chain L Focus chain M [auth L] Focus chain N [auth L] Focus chain O [auth L] Focus chain P [auth L] Focus chain Q [auth L] Focus chain R [auth L] Focus chain S [auth L] Interactions & Density Focus chain J [auth L] Focus chain K [auth L] Focus chain L Focus chain M [auth L] Focus chain N [auth L] Focus chain O [auth L] Focus chain P [auth L] Focus chain Q [auth L] Focus chain R [auth L] Focus chain S [auth L]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain I [auth L] MOL2 format, chain I [auth L] mmCIF format, chain I [auth L]	I [auth L]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain I [auth L] Interactions & Density Focus chain I [auth L]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain H [auth L] MOL2 format, chain H [auth L] mmCIF format, chain H [auth L]	H [auth L]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain H [auth L] Interactions & Density Focus chain H [auth L]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain F [auth L] SDF format, chain G [auth L] MOL2 format, chain F [auth L] MOL2 format, chain G [auth L] mmCIF format, chain F [auth L] mmCIF format, chain G [auth L]	F [auth L], G [auth L]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth L] Focus chain G [auth L] Interactions & Density Focus chain F [auth L] Focus chain G [auth L]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 8
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000459 (TCK) Query on PRD_000459	U [auth L]	Tosyl-L-lysine chloromethyl ketone	Peptide-like / Inhibitor		Interactions Focus chain U [auth L] Interactions & Density Focus chain U [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.145 (Depositor), 0.150 (DCC)
R-Value Work: 0.120 (Depositor), 0.127 (DCC)
R-Value Observed: 0.122 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 116.941	α = 90
b = 116.941	β = 90
c = 86.852	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Blu-Ice	data collection
SHELX	phasing
Coot	model building
Aimless	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-12-31

Deposition Author(s):

Gorman, M.A.

Parker, M.W.

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
Version 1.5: 2023-12-27
Changes: Data collection, Database references, Derived calculations
Version 1.6: 2024-11-06
Changes: Structure summary