7M1Z

Targeting Enterococcus faecalis HMG-CoA reductase with a novel non-statin inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HMGClick on this verticalbar to view detailsBest fitted NAPClick on this verticalbar to view details

This is version 1.2 of the entry. See complete history


Literature

Targeting Enterococcus faecalis HMG-CoA reductase with a non-statin inhibitor

Bose, S.Steussy, C.N.Lopez-Perez, D.Schmidt, T.Kulathunga, S.C.Seleem, M.N.Lipton, M.Mesecar, A.D.Rodwell, V.W.Stauffacher, C.V.

(2023) Nat Commun 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Hydroxymethylglutaryl-CoA reductase, degradative
A, B, C, D
430Enterococcus faecalisMutation(s): 0 
Gene Names: G5T22_00100
EC: 1.1.1.88 (PDB Primary Data), 2.3.1.9 (UniProt)
UniProt
Find proteins for Q835L3 (Enterococcus faecalis (strain ATCC 700802 / V583))
Explore Q835L3 
Go to UniProtKB:  Q835L3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ835L3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HMG
Query on HMG

Download Ideal Coordinates CCD File 
Q [auth B]3-HYDROXY-3-METHYLGLUTARYL-COENZYME A
C27 H39 N7 O20 P3 S
CABVTRNMFUVUDM-VRHQGPGLSA-I
NAP
Query on NAP

Download Ideal Coordinates CCD File 
E [auth A],
EA [auth D],
R [auth B],
X [auth C]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
MEV
Query on MEV

Download Ideal Coordinates CCD File 
W [auth C](R)-MEVALONATE
C6 H11 O4
KJTLQQUUPVSXIM-ZCFIWIBFSA-M
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
S [auth B]
T [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
CA [auth C]
DA [auth C]
K [auth A]
L [auth A]
M [auth A]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
FA [auth D]
GA [auth D]
I [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 241.289α = 90
b = 62.557β = 133.49
c = 171.925γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted HMGClick on this verticalbar to view detailsBest fitted NAPClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesHL52115
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesMH082373

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-21
    Type: Initial release
  • Version 1.1: 2023-04-05
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description