8E7P

Staphylococcus aureus ClpP in complex with compound 3421


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Development of a high throughput and site specific, fluorescent polarization assay to screen for activators of Caseinolytic Protease P leads to the discovery of synthetically tractable new activator class

Singh, A.C.Zhao, Y.Griffith, E.C.Tangallapally, R.Jarret, M.W.Lee, R.E.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent Clp protease proteolytic subunit203Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: clpPSAOUHSC_00790
EC: 3.4.21.92
UniProt
Find proteins for Q2G036 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2G036 
Go to UniProtKB:  Q2G036
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2G036
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UTC (Subject of Investigation/LOI)
Query on UTC

Download Ideal Coordinates CCD File 
AA [auth G]
DA [auth I]
EA [auth K]
GA [auth L]
IA [auth M]
AA [auth G],
DA [auth I],
EA [auth K],
GA [auth L],
IA [auth M],
KA [auth N],
MA [auth S],
OA [auth S],
P [auth A],
Q [auth B],
S [auth C],
W [auth D],
Y [auth F]
(5R,6S,9aS)-N-benzyl-6-[(4-hydroxyphenyl)methyl]-8-[(naphthalen-1-yl)methyl]-4,7-dioxohexahydro-2H-pyrazino[1,2-a]pyrimidine-1(6H)-carboxamide
C33 H32 N4 O4
HQWTUOLCGKIECB-XZWHSSHBSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
BA [auth G]
CA [auth I]
FA [auth K]
HA [auth L]
JA [auth M]
BA [auth G],
CA [auth I],
FA [auth K],
HA [auth L],
JA [auth M],
LA [auth N],
NA [auth S],
O [auth A],
PA [auth T],
R [auth B],
T [auth C],
U [auth D],
V [auth D],
X [auth E],
Z [auth F]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.073α = 90
b = 126.143β = 93.88
c = 145.475γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI110578

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-05
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description