1YVM

E. coli Methionine Aminopeptidase in complex with thiabendazole

• PDB DOI: https://doi.org/10.2210/pdb1YVM/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2005-02-16 Released: 2005-06-07 
• Deposition Author(s): Schiffmann, R., Heine, A., Klebe, G., Klein, C.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.233 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 

Literature

Metal Ions as Cofactors for the Binding of Inhibitors to Methionine Aminopeptidase: A Critical View of the Relevance of In Vitro Metalloenzyme Assays.

Schiffmann, R., Heine, A., Klebe, G., Klein, C.D.

(2005) Angew Chem Int Ed Engl 44: 3620-3623

• PubMed: 15880695 
• DOI: https://doi.org/10.1002/anie.200500592
• Primary Citation of Related Structures:  
  1YVM

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Organizational Affiliation: 

FR 8.2 Pharmazeutische und Medizinische Chemie, Saarland University, 66041 Saarbrücken, Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 29.8 kDa 
• Atom Count: 2,345 
• Modelled Residue Count: 262 
• Deposited Residue Count: 264 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine aminopeptidase	A	264	Escherichia coli	Mutation(s): 1  Gene Names: map EC: 3.4.11.18
UniProt
Find proteins for P0AE18 (Escherichia coli (strain K12)) Explore P0AE18  Go to UniProtKB:  P0AE18

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TMG	G [auth A]	2-(1,3-THIAZOL-4-YL)-1H-BENZIMIDAZOLE C10 H7 N3 S WJCNZQLZVWNLKY-UHFFFAOYSA-N
CO	B [auth A], C [auth A], D [auth A], E [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N
NA	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
TMG	PDBBind:  1YVM	Ki: 400 (nM) from 1 assay(s)
	Binding MOAD:  1YVM	Ki: 400 (nM) from 1 assay(s)
	BindingDB:  1YVM	IC50: 472 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.233 
• R-Value Work: 0.168 
• R-Value Observed: 0.170 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.91	α = 90
b = 66.13	β = 111.25
c = 48.53	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
CrystalClear	data reduction
HKL-2000	data scaling
PHASER	phasing
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-06-07 
Deposition Author(s): Schiffmann, R., Heine, A., Klebe, G., Klein, C.D.

Revision History  

• Version 1.0: 2005-06-07
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.4: 2023-08-23
  Changes: Data collection, Refinement description