1XRY | pdb_00001xry

Crystal structure of Aeromonas proteolytica aminopeptidase in complex with bestatin

• PDB DOI: https://doi.org/10.2210/pdb1XRY/pdb

• Classification: HYDROLASE
• Organism(s): Vibrio proteolyticus
• Mutation(s): No 


• Deposited: 2004-10-17 Released: 2005-09-27 
• Deposition Author(s): Gilboa, R., Rondeau, J.-M., Blumberg, S., Tarnus, C., Shoham, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.197 (Depositor), 0.192 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Interactions of Streptomyces griseus Aminopeptidase and Aeromonas proteolytica Aminopeptidase with Bestatin. Structural analysis of homologous enzymes with different binding modes.

Gilboa, R., Rondeau, J.-M., Blumberg, S., Tarnus, C., Shoham, G.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 32.68 kDa 
• Atom Count: 2,406 
• Modeled Residue Count: 291 
• Deposited Residue Count: 299 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacterial leucyl aminopeptidase	A	299	Vibrio proteolyticus	Mutation(s): 0  EC: 3.4.11.10
UniProt
Find proteins for Q01693 (Vibrio proteolyticus) Explore Q01693  Go to UniProtKB:  Q01693

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BES	D [auth A]	2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID C16 H24 N2 O4 VGGGPCQERPFHOB-RDBSUJKOSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.197 (Depositor), 0.192 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.39	α = 90
b = 107.39	β = 90
c = 103.06	γ = 120

Software Package:

Software Name	Purpose
CNX	refinement
X-GEN	data reduction
XDS	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-09-27 
Deposition Author(s): Gilboa, R., Rondeau, J.-M., Blumberg, S., Tarnus, C., Shoham, G.

Revision History  

• Version 1.0: 2005-09-27
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-30
  Changes: Structure summary