E. coli methionine aminopeptidase Mn-form with inhibitor B21

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.226 

Starting Model: experimental
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Structural analysis of inhibition of E. coli methionine aminopeptidase: implication of loop flexibility in selective inhibition of bacterial enzymes.

Ma, Z.Q.Xie, S.X.Huang, Q.Q.Nan, F.J.Hurley, T.D.Ye, Q.Z.

(2007) BMC Struct Biol 7: 84-84

  • DOI: https://doi.org/10.1186/1472-6807-7-84
  • Primary Citation of Related Structures:  
    2Q92, 2Q93, 2Q94, 2Q95, 2Q96

  • PubMed Abstract: 

    Methionine aminopeptidase is a potential target of future antibacterial and anticancer drugs. Structural analysis of complexes of the enzyme with its inhibitors provides valuable information for structure-based drug design efforts. Five new X-ray structures of such enzyme-inhibitor complexes were obtained. Analysis of these and other three similar structures reveals the adaptability of a surface-exposed loop bearing Y62, H63, G64 and Y65 (the YHGY loop) that is an integral part of the substrate and inhibitor binding pocket. This adaptability is important for accommodating inhibitors with variations in size. When compared with the human isozymes, this loop either becomes buried in the human type I enzyme due to an N-terminal extension that covers its position or is replaced by a unique insert in the human type II enzyme. The adaptability of the YHGY loop in E. coli methionine aminopeptidase, and likely in other bacterial methionine aminopeptidases, enables the enzyme active pocket to accommodate inhibitors of differing size. The differences in this adaptable loop between the bacterial and human methionine aminopeptidases is a structural feature that can be exploited to design inhibitors of bacterial methionine aminopeptidases as therapeutic agents with minimal inhibition of the corresponding human enzymes.

  • Organizational Affiliation

    High Throughput Screening Laboratory, University of Kansas, Lawrence, Kansas 66047, USA. zeqiang.ma@vanderbilt.edu

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Methionine aminopeptidase263Escherichia coliMutation(s): 0 
Gene Names: map
Find proteins for P0AE18 (Escherichia coli (strain K12))
Explore P0AE18 
Go to UniProtKB:  P0AE18
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AE18
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
B21 BindingDB:  2Q93 IC50: min: 558, max: 2.00e+5 (nM) from 3 assay(s)
PDBBind:  2Q93 IC50: 560 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.226 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.107α = 90
b = 62.34β = 108.8
c = 52.441γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2008-01-01 
  • Deposition Author(s): Ye, Q.-Z.

Revision History  (Full details and data files)

  • Version 1.0: 2008-01-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description