6BOI

Crystal Structure of LdtMt2 (56-408) with a panipenem adduct at the active site cysteine-354


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.102 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structures and Mechanism of Inhibition of Mycobacterium tuberculosis L,D-transpeptidase 2 by Panipenem

Saavedra, H.Bianchet, M.A.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative conserved lipoprotein LppS
A, B
352Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra)Mutation(s): 0 
Gene Names: lppS
Find proteins for A5U5L6 (Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra))
Go to UniProtKB:  A5U5L6
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 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
E0Y
Query on E0Y

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A, B
(3S,5R)-5-[(2R,3R)-1,3-dihydroxybutan-2-yl]-3-({(3R)-1-[(1E)-ethanimidoyl]pyrrolidin-3-yl}sulfanyl)-L-proline
C15 H27 N3 O4 S
BSDSVSWWQWOWPI-SXFXLBHASA-N
 Ligand Interaction
PEG
Query on PEG

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A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.102 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 61.060α = 90.00
b = 94.060β = 92.70
c = 75.400γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PHENIXphasing
PHENIXrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-04-11
    Type: Initial release