4Z7M | pdb_00004z7m

Novel Inhibitors of Bacterial Methionine Aminopeptidase with Broad-Spectrum Biochemical Activity

• PDB DOI: https://doi.org/10.2210/pdb4Z7M/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-04-07 Released: 2016-04-13 
• Deposition Author(s): Rose, J.A., Lahiri, S.D., McKinney, D.C., Albert, R., Morningstar, M., Shapiro, A.B., Fisher, S.F., Fleming, P.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free: 
  0.305 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.251 (Depositor), 0.260 (DCC) 
• R-Value Observed: 
  0.254 (Depositor) 

Literature

Novel Inhibitors of Bacterial Methionine Aminopeptidase with Broad-Spectrum Biochemical Activity

Rose, J.A., Lahiri, S.D., McKinney, D.C., Albert, R., Morningstar, M., Shapiro, A.B., Fisher, S.F., Fleming, P.R.

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: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 58.98 kDa 
• Atom Count: 4,505 
• Modeled Residue Count: 522 
• Deposited Residue Count: 522 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine aminopeptidase	A, B	261	Escherichia coli	Mutation(s): 0  Gene Names: map, Z0178, ECs0170 EC: 3.4.11.18
UniProt
Find proteins for P0AE18 (Escherichia coli (strain K12)) Explore P0AE18  Go to UniProtKB:  P0AE18

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4L9	D [auth A], F [auth B]	N~2~-[(3,5-difluorophenyl)acetyl]-N-[(3S,7R)-1-methyl-2-oxo-7-phenyl-2,3,4,7-tetrahydro-1H-azepin-3-yl]-L-alaninamide C24 H25 F2 N3 O3 XGCLGFYBNGRVHO-ONGXBYRLSA-N
MN	C [auth A], E [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.43 Å
• R-Value Free:  0.305 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.251 (Depositor), 0.260 (DCC) 
• R-Value Observed: 0.254 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.985	α = 90
b = 62.712	β = 89.59
c = 72.978	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
d*TREK	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-13 
Deposition Author(s): Rose, J.A., Lahiri, S.D., McKinney, D.C., Albert, R., Morningstar, M., Shapiro, A.B., Fisher, S.F., Fleming, P.R.

Revision History  

• Version 1.0: 2016-04-13
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Data collection, Database references, Derived calculations