1HS6 | pdb_00001hs6

STRUCTURE OF LEUKOTRIENE A4 HYDROLASE COMPLEXED WITH BESTATIN.


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report

Validation slider image for 1HS6

This is version 1.4 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: https://doi.org/10.1038/84117
  • Primary Citation 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. 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

Macromolecule Content 

  • Total Structure Weight: 70.38 kDa 
  • Atom Count: 5,462 
  • Modeled Residue Count: 610 
  • Deposited Residue Count: 611 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
LEUKOTRIENE A-4 HYDROLASE611Homo sapiensMutation(s): 0 
EC: 3.3.2.6 (PDB Primary Data), 3.4.11.4 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P09960 (Homo sapiens)
Explore P09960 
Go to UniProtKB:  P09960
PHAROS:  P09960
GTEx:  ENSG00000111144 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09960
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BES

Query on BES



Download:Ideal Coordinates CCD File
G [auth A]2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID
C16 H24 N2 O4
VGGGPCQERPFHOB-RDBSUJKOSA-N
YB

Query on YB



Download:Ideal Coordinates CCD File
C [auth A],
D [auth A],
E [auth A]
YTTERBIUM (III) ION
Yb
AWSFICBXMUKWSK-UHFFFAOYSA-N
IMD

Query on IMD



Download:Ideal Coordinates CCD File
H [auth A]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN

Query on ZN



Download:Ideal Coordinates CCD File
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
F [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

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

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references, Derived calculations