4BGE | pdb_00004bge

Crystal structure of InhA(S94A) mutant in complex with pyridomycin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 
    0.278 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.240 (Depositor), 0.262 (DCC) 
  • R-Value Observed: 
    0.242 (Depositor) 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history. 

Literature

Pyridomycin bridges the NADH- and substrate-binding pockets of the enoyl reductase InhA.

Hartkoorn, R.C., Pojer, F., Read, J.A., Gingell, H., Neres, J., Horlacher, O.P., Altmann, K.H., Cole, S.T.

(2014) Nat Chem Biol 10: 96-98

  • DOI: https://doi.org/10.1038/nchembio.1405
  • Primary Citation Related Structures: 
    4BGE, 4BGI, 4BII

  • PubMed Abstract: 

    Pyridomycin, a natural product with potent antituberculosis activity, inhibits a major drug target, the InhA enoyl reductase. Here, we unveil the co-crystal structure and unique ability of pyridomycin to block both the NADH cofactor- and lipid substrate-binding pockets of InhA. This is to our knowledge a first-of-a-kind binding mode that discloses a new means of InhA inhibition. Proof-of-principle studies show how structure-assisted drug design can improve the activity of new pyridomycin derivatives.

    • Organizational Affiliation: 
    • Ecole Polytechnique Fédérale de Lausanne, Global Health Institute, Lausanne, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 174.48 kDa 
  • Atom Count: 12,612 
  • Modeled Residue Count: 1,558 
  • Deposited Residue Count: 1,614 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Enoyl-[acyl-carrier-protein] reductase [NADH]
A, B, C, D, E
A, B, C, D, E, F
269Mycobacterium tuberculosis H37RvMutation(s): 1 
Gene Names: inhA, Rv1484, MTCY277.05
EC: 1.3.1.9
UniProt
Find proteins for P9WGR1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WGR1 
Go to UniProtKB:  P9WGR1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WGR1
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free:  0.278 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.240 (Depositor), 0.262 (DCC) 
  • R-Value Observed: 0.242 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.601α = 90
b = 83.049β = 94.84
c = 190.682γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-04
    Type: Initial release
  • Version 1.1: 2013-12-11
    Changes: Database references
  • Version 1.2: 2014-02-05
    Changes: Database references
  • Version 1.3: 2018-11-21
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.4: 2019-10-16
    Changes: Data collection, Other
  • Version 1.5: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description