1T02 | pdb_00001t02

Crystal structure of a Statin bound to class II HMG-CoA reductase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.251 (Depositor) 
  • R-Value Work: 
    0.196 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Crystal structure of a statin bound to a class II hydroxymethylglutaryl-CoA reductase.

Tabernero, L.Rodwell, V.W.Stauffacher, C.V.

(2003) J Biological Chem 278: 19933-19938

  • DOI: https://doi.org/10.1074/jbc.M213006200
  • Primary Citation Related Structures: 
    1T02

  • PubMed Abstract: 

    Hydroxymethylglutaryl-CoA (HMG-CoA) reductase is the primary target in the current clinical treatment of hypercholesterolemias with specific inhibitors of the "statin" family. Statins are excellent inhibitors of the class I (human) enzyme but relatively poor inhibitors of the class II enzymes of important bacterial pathogens. To investigate the molecular basis for this difference we determined the x-ray structure of the class II Pseudomonas mevalonii HMG-CoA reductase in complex with the statin drug lovastatin. The structure shows lovastatin bound in the active site and its interactions with residues critically involved in catalysis and substrate binding. Binding of lovastatin also displaces the flap domain of the enzyme, which contains the catalytic residue His-381. Comparison with the structures of statins bound to the human enzyme revealed a similar mode of binding but marked differences in specific interactions that account for the observed differences in affinity. We suggest that these differences might be exploited to develop selective class II inhibitors for use as antibacterial agents against pathogenic microorganisms.


  • Organizational Affiliation
    • School of Biological Sciences, University of Manchester, Oxford Road, United Kingdom. Lydia.Tabernero@man.ac.uk

Macromolecule Content 

  • Total Structure Weight: 91.8 kDa 
  • Atom Count: 5,654 
  • Modeled Residue Count: 745 
  • Deposited Residue Count: 856 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
3-hydroxy-3-methylglutaryl-coenzyme A reductase
A, B
428Pseudomonas sp. 'mevaloniiMutation(s): 0 
Gene Names: MVAA
EC: 1.1.1.88
UniProt
Find proteins for P13702 (Pseudomonas mevalonii)
Explore P13702 
Go to UniProtKB:  P13702
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13702
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LVA

Query on LVA



Download:Ideal Coordinates CCD File
C [auth A](3R,5R)-7-((1R,2R,6S,8R,8AS)-2,6-DIMETHYL-8-{[(2R)-2-METHYLBUTANOYL]OXY}-1,2,6,7,8,8A-HEXAHYDRONAPHTHALEN-1-YL)-3,5-DIHYDROXYHEPTANOIC ACID
C24 H38 O6
QLJODMDSTUBWDW-BXMDZJJMSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.251 (Depositor) 
  • R-Value Work:  0.196 (Depositor) 
Space Group: I 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 228.5α = 90
b = 228.5β = 90
c = 228.5γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-08-03
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2015-01-21
    Changes: Refinement description
  • Version 1.4: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description