3EBI

Structure of the M1 Alanylaminopeptidase from malaria complexed with the phosphinate dipeptide analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.221
  • R-Value Work: 0.175

Literature

Macromolecules
Sequence Display for 3EBI

Classification: HYDROLASE INHIBITOR

Total Structure Weight: 104745.19

Macromolecule Entities
Molecule Chains Length Organism Details
M1 family aminopeptidase A 890 Plasmodium falciparum EC#: 3.4.11 IUBMB
Fragment: UNP residues 195 to 1084
Mutation: N213Q, N223Q, H378P, N501Q, N745Q, N795Q, N1069Q
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
BEY
Query on BEY

A (2S)-3-[(R)-[(1S)-1-amino-3-phenylpropyl](hydroxy)phosphoryl]- 2-benzylpropanoic acid
C19 H24 N O4 P
QELOIXSGJMIHBZ-MSOLQXFVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
BEY N/A in BindingDB
Ki: 79 nM  BindingMOAD
Ki: 79 nM  PDBbind

Experimental Data & Validation

Experimental Data

Unit Cell:

Length (Å) Angle (°)
a = 75.85 α = 90.00
b = 108.63 β = 90.00
c = 118.32 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-08-27
  • Released Date: 2009-01-27
  • Deposition author(s): McGowan, S., Porter, C.J., Buckle, A.M., Whisstock, J.C.

Revision History

  • 2011-07-13
    Type: Non-polymer description, Version format compliance