2EK9 | pdb_00002ek9

Aminopeptidase from Aneurinibacillus sp. strain AM-1 with Bestatin

• PDB DOI: https://doi.org/10.2210/pdb2EK9/pdb

• Classification: HYDROLASE
• Organism(s): Aneurinibacillus sp. AM-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-03-22 Released: 2008-03-25 
• Deposition Author(s): Akioka, M., Nakano, H., Watanabe, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 
  0.219 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Model: experimental

Literature

Structural characterization of a novel bacterial aminopeptidase with an apical domain from aneurinibacillus sp. strain AM-1

Akioka, M., Nakano, H., Tsujimoto, Y., Matsui, H., Nakatsu, T., Kato, H., Watanabe, K.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 46.05 kDa 
• Atom Count: 3,655 
• Modeled Residue Count: 412 
• Deposited Residue Count: 421 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminopeptidase	A	421	Aneurinibacillus sp. AM-1	Mutation(s): 0
UniProt
Find proteins for A2V759 (Aneurinibacillus sp. AM-1) Explore A2V759  Go to UniProtKB:  A2V759

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BES	H [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], D [auth A], E [auth A], F [auth A], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
IPA	I [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.219 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.813	α = 90
b = 68.678	β = 90
c = 77.044	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
CrystalClear	data collection
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-25 
Deposition Author(s): Akioka, M., Nakano, H., Watanabe, K.

Revision History  

• Version 1.0: 2008-03-25
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description