6P4E

Leishmania mexicana CPB in complex with an aza-nitrile inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

wwPDB Validation 3D Report Full Report



Literature

High Resolution X-Ray Crystal Structures of LmCPB2.8 Co-Crystalized with Dipeptidyl Aza-nitrile Inhibitor and Structure Activity Relationships

Ribeiro, J.F.R.De Vita, D.Li, C.Emsley, J.Montanari, C.A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cysteine proteinase BAB217Leishmania mexicanaMutation(s): 3 
Gene Names: LMCPBLMCPB2.8
EC: 3.4.22
Find proteins for P36400 (Leishmania mexicana)
Explore P36400 
Go to UniProtKB:  P36400
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GES
Query on GES

Download CCD File 
A, B
3-tert-butyl-N-[(2S)-1-(2-cyano-1,2-dimethylhydrazinyl)-4-methyl-1-oxopentan-2-yl]-1-methyl-1H-pyrazole-5-carboxamide (non-preferred name)
C18 H30 N6 O2
BTSJGBRRCQOXFA-ZDUSSCGKSA-N
 Ligand Interaction
TRS
Query on TRS

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B
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
MPD
Query on MPD

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A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
ACT
Query on ACT

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A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

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A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.636α = 90
b = 82.636β = 90
c = 134.846γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentBrazilCAPES AUXPE 139/2015

Revision History 

  • Version 1.0: 2020-06-03
    Type: Initial release