6I9A

Porphyromonas gingivalis gingipain K (Kgp) in complex with inhibitor KYT-36


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.146 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural determinants of inhibition of Porphyromonas gingivalis gingipain K by KYT-36, a potent, selective, and bioavailable peptidase inhibitor.

Guevara, T.Rodriguez-Banqueri, A.Lasica, A.M.Ksiazek, M.Potempa, B.A.Potempa, J.Gomis-Ruth, F.X.

(2019) Sci Rep 9: 4935-4935


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lys-gingipain W83
A, B
461Porphyromonas gingivalisMutation(s): 0 
Gene Names: kgp (prtK, prtP)
EC: 3.4.22.47
Find proteins for Q51817 (Porphyromonas gingivalis)
Go to UniProtKB:  Q51817
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

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A, B
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

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A, B
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
DTV
Query on DTV

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B
(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL
C4 H10 O2 S2
VHJLVAABSRFDPM-QWWZWVQMSA-N
 Ligand Interaction
H8E
Query on H8E

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A, B
benzyl-N-[(2S)-1-[[(3S)-7-amino-1-(benzylamino)-1,2-dioxoheptan-3-yl]amino]-5-(2-methyl-2-phenylhydrazinyl)-1,5-dioxopentan-2-yl]carbamate
C34 H42 N6 O6
XDVSKHGOOXWVDB-VMPREFPWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.148 
  • R-Value Work: 0.146 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.670α = 90.00
b = 87.050β = 90.00
c = 129.210γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
BUSTERrefinement
PHASERphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-03-13
    Type: Initial release
  • Version 1.1: 2019-03-20
    Type: Data collection, Refinement description
  • Version 1.2: 2019-03-27
    Type: Data collection, Refinement description
  • Version 1.3: 2019-04-03
    Type: Data collection, Database references