5IB9 | pdb_00005ib9

Crystal structure of aminopeptidase equipped with PAD from Aneurinibacillus sp. AM-1

• PDB DOI: https://doi.org/10.2210/pdb5IB9/pdb

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


• Deposited: 2016-02-22 Released: 2017-02-22 
• Deposition Author(s): Tagawa, R., Nakano, H., Watanabe, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of aminopeptidase

Tagawa, R., Nakano, H., Watanabe, K.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 45.99 kDa 
• Atom Count: 3,737 
• 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  Gene Names: amp
UniProt
Find proteins for A2V759 (Aneurinibacillus sp. AM-1) Explore A2V759  Go to UniProtKB:  A2V759

Small Molecules

Ligands 2 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.18	α = 90
b = 68.443	β = 90
c = 76.589	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-02-22 
Deposition Author(s): Tagawa, R., Nakano, H., Watanabe, K.

Revision History  

• Version 1.0: 2017-02-22
  Type: Initial release
  
• Version 1.1: 2020-02-19
  Changes: Data collection
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description