1HS6

STRUCTURE OF LEUKOTRIENE A4 HYDROLASE COMPLEXED WITH BESTATIN.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Crystal structure of human leukotriene A(4) hydrolase, a bifunctional enzyme in inflammation.

Thunnissen, M.M., Nordlund, P., Haeggstrom, J.Z.

(2001) Nat Struct Biol 8: 131-135

  • DOI: 10.1038/84117
  • Primary Citation of Related Structures:  
    1HS6

  • PubMed Abstract: 

    • Leukotriene (LT) A(4) hydrolase/aminopeptidase (LTA4H) is a bifunctional zinc enzyme that catalyzes the biosynthesis of LTB4, a potent lipid chemoattractant involved in inflammation, immune responses, host defense against infection, and PAF-induced shock ...

    Leukotriene (LT) A(4) hydrolase/aminopeptidase (LTA4H) is a bifunctional zinc enzyme that catalyzes the biosynthesis of LTB4, a potent lipid chemoattractant involved in inflammation, immune responses, host defense against infection, and PAF-induced shock. The high resolution crystal structure of LTA4H in complex with the competitive inhibitor bestatin reveals a protein folded into three domains that together create a deep cleft harboring the catalytic Zn(2+) site. A bent and narrow pocket, shaped to accommodate the substrate LTA(4), constitutes a highly confined binding region that can be targeted in the design of specific anti-inflammatory agents. Moreover, the structure of the catalytic domain is very similar to that of thermolysin and provides detailed insight into mechanisms of catalysis, in particular the chemical strategy for the unique epoxide hydrolase reaction that generates LTB(4).

    Organizational Affiliation: 

    Department of Biochemistry, University of Stockholm, Arrhenius Laboratories A4, S-106 91 Stockholm, Sweden. marjo@dbb.su.se



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LEUKOTRIENE A-4 HYDROLASE A611Homo sapiensMutation(s): 0 
Gene Names: LTA4H, LTA4
EC: 3.3.2.6 (PDB Primary Data), 3.4.11.4 (UniProt)
Find proteins for P09960 (Homo sapiens)
Explore P09960 
Go to UniProtKB:  P09960
NIH Common Fund Data Resources
PHAROS:  P09960
GTEx:  ENSG00000111144
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BES
Query on BES
Download Ideal Coordinates CCD File 
A
2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID
C16 H24 N2 O4
VGGGPCQERPFHOB-RDBSUJKOSA-N		 Ligand Interaction
YB
Query on YB
Download Ideal Coordinates CCD File 
A
YTTERBIUM (III) ION
Yb
AWSFICBXMUKWSK-UHFFFAOYSA-N		 Ligand Interaction
IMD
Query on IMD
Download Ideal Coordinates CCD File 
A
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
ACT
Query on ACT
Download Ideal Coordinates CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BESIC50:  300   nM  BindingDB
BESIC50:  20000   nM  BindingDB
BESIC50:  10100   nM  BindingDB
BESIC50 :  4200   nM  PDBBind
BESKd:  2050   nM  BindingDB
BESIC50:  500   nM  BindingDB
BESIC50:  4000   nM  BindingDB
BESKd:  4630   nM  BindingDB
BESIC50:  4200   nM  BindingDB
BESIC50:  18010   nM  BindingDB
BESKd:  5150   nM  BindingDB
BESKi:  320   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.6α = 90
b = 133.5β = 90
c = 83.4γ = 90
Software Package:
Software NamePurpose
MLPHAREphasing
SHARPphasing
TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-06-24
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-11-20
    Changes: Derived calculations