5YO1

Structure of ePepN E298A mutant in complex with Puromycin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.129 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminopeptidase N891Escherichia coli K-12Mutation(s): 1 
Gene Names: pepNb0932JW0915
EC: 3.4.11.2
UniProt
Find proteins for P04825 (Escherichia coli (strain K12))
Explore P04825 
Go to UniProtKB:  P04825
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04825
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PUY (Subject of Investigation/LOI)
Query on PUY

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
PUROMYCIN
C22 H29 N7 O5
RXWNCPJZOCPEPQ-NVWDDTSBSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA
Query on NA

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E [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.129 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.325α = 90
b = 120.325β = 90
c = 170.012γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
IndiaBT-BRB-TF-2-2011

Revision History  (Full details and data files)

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