5Y1S

Crystal structure of Plasmodium falciparum aminopeptidase N in complex with (S)-2-(3-(3,4-dimethylbenzyl)ureido)-N-hydroxy-4-methylpentanamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of Plasmodium falciparum aminopeptidase N in complex with (S)-2-(3-(3,4-dimethylbenzyl)ureido)-N-hydroxy-4-methylpentanamide

Marapaka, A.K.Addlagatta, A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
M1 family aminopeptidase914Plasmodium falciparum FcB1/ColumbiaMutation(s): 0 
EC: 3.4.11
UniProt
Find proteins for O96935 (Plasmodium falciparum (isolate 3D7))
Explore O96935 
Go to UniProtKB:  O96935
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO96935
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
E8R
Query on E8R

Download Ideal Coordinates CCD File 
G [auth A](2R)-2-[(3,4-dimethylphenyl)methylcarbamoylamino]-4-methyl-N-oxidanyl-pentanamide
C16 H25 N3 O3
OPDKYCNMBLFHGN-CQSZACIVSA-N
E8F
Query on E8F

Download Ideal Coordinates CCD File 
F [auth A](2S)-2-[(3,4-dimethylphenyl)methylcarbamoylamino]-4-methyl-N-oxidanyl-pentanamide
C16 H25 N3 O3
OPDKYCNMBLFHGN-AWEZNQCLSA-N
GOL
Query on GOL

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H [auth A],
I [auth A],
J [auth A],
K [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

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B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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C [auth A],
D [auth A],
E [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.699α = 90
b = 109.405β = 90
c = 112.991γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata collection
SCALEPACKdata scaling
MOLREPmodel building
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description