5YQB | pdb_00005yqb

Crystal structure of E.coli aminopeptidase N in complex with Puromycin

• PDB DOI: https://doi.org/10.2210/pdb5YQB/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-11-06 Released: 2018-11-14 
• Deposition Author(s): Marapaka, A.K., Ganji, R.J., Reddi, R., Addlagatta, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free: 
  0.182 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.162 (Depositor) 

Starting Model: experimental

Literature

Puromycin, a selective inhibitor of PSA acts as a substrate for other M1 family aminopeptidases: Biochemical and structural basis

Reddi, R., Ganji, R.J., Marapaka, A.K., Bala, S.C., Yerra, N.V., Haque, N., Addlagatta, A.

(2020) Int J Biol Macromol 165: 1373-1381

• DOI: https://doi.org/10.1016/j.ijbiomac.2020.10.035

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 101.98 kDa 
• Atom Count: 7,949 
• Modeled Residue Count: 866 
• Deposited Residue Count: 891 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Aminopeptidase N	A	891	Escherichia coli K-12	Mutation(s): 0  Gene Names: pepN, b0932, JW0915 EC: 3.4.11.2
UniProt
Find proteins for P04825 (Escherichia coli (strain K12)) Explore P04825  Go to UniProtKB:  P04825

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GMC	D [auth A]	(2R,3R,4S,5S)-4-AMINO-2-[6-(DIMETHYLAMINO)-9H-PURIN-9-YL]-5-(HYDROXYMETHYL)TETRAHYDRO-3-FURANOL C12 H18 N6 O3 RYSMHWILUNYBFW-GRIPGOBMSA-N
0A1	C [auth A]	O-methyl-L-tyrosine C10 H13 N O3 GEYBMYRBIABFTA-VIFPVBQESA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free:  0.182 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.162 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.292	α = 90
b = 120.292	β = 90
c = 170.123	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data collection
SCALEPACK	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction
Coot	model building
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-11-14 
Deposition Author(s): Marapaka, A.K., Ganji, R.J., Reddi, R., Addlagatta, A.

Revision History  

• Version 1.0: 2018-11-14
  Type: Initial release
  
• Version 1.1: 2022-07-27
  Changes: Database references, Refinement description
• Version 1.2: 2023-11-22
  Changes: Data collection, Refinement description