6P4E | pdb_00006p4e

Leishmania mexicana CPB in complex with an aza-nitrile inhibitor

• PDB DOI: https://doi.org/10.2210/pdb6P4E/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Leishmania mexicana
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-05-27 Released: 2020-06-03 
• Deposition Author(s): Ribeiro, J.F.R., Li, C., De Vita, D., Emsley, J., Montanari, C.A.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 
  0.213 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 47.9 kDa 
• Atom Count: 4,011 
• Modeled Residue Count: 433 
• Deposited Residue Count: 434 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cysteine proteinase B	A, B	217	Leishmania mexicana	Mutation(s): 3  Gene Names: LMCPB, LMCPB2.8 EC: 3.4.22
UniProt
Find proteins for P36400 (Leishmania mexicana) Explore P36400  Go to UniProtKB:  P36400

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GES (Subject of Investigation/LOI)	H [auth A], O [auth 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
TRS	N [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
MPD	F [auth A], G [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
ACT	D [auth A], E [auth A], J [auth B], K [auth B], L [auth B], M [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	C [auth A], I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free:  0.213 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.636	α = 90
b = 82.636	β = 90
c = 134.846	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-06-03 
Deposition Author(s): Ribeiro, J.F.R., Li, C., De Vita, D., Emsley, J., Montanari, C.A.

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Funding Organization	Location	Grant Number
Other government	Brazil	CAPES AUXPE 139/2015

Revision History  

• Version 1.0: 2020-06-03
  Type: Initial release
  
• Version 1.1: 2023-02-01
  Changes: Advisory, Database references, Derived calculations
• Version 1.2: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.3: 2024-12-25
  Changes: Advisory, Derived calculations, Structure summary