5FWQ | pdb_00005fwq

Apo structure of human Leukotriene A4 hydrolase

• PDB DOI: https://doi.org/10.2210/pdb5FWQ/pdb

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


• Deposited: 2016-02-19 Released: 2016-10-05 
• Deposition Author(s): Wittmann, S.K., Kalinowsky, L., Kramer, J., Bloecher, R., Steinhilber, D., Pogoryelov, D., Proschak, E., Heering, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.223 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Thermodynamic properties of leukotriene A4hydrolase inhibitors.

Wittmann, S.K., Kalinowsky, L., Kramer, J.S., Bloecher, R., Knapp, S., Steinhilber, D., Pogoryelov, D., Proschak, E., Heering, J.

(2016) Bioorg Med Chem 24: 5243-5248

• PubMed: 27651294 
• DOI: https://doi.org/10.1016/j.bmc.2016.08.047
• Primary Citation Related Structures: 
  5FWQ


• PubMed Abstract: 
  

  The leukotriene A ₄ hydrolase (LTA ₄ H) is a bifunctional enzyme, containing a peptidase and a hydrolase activity both activities having opposing functions regulating inflammatory response. The hydrolase activity is responsible for the conversion of leukotriene A ₄ to pro-inflammatory leukotriene B ₄ , and hence, selective inhibitors of the hydrolase activity are of high pharmacological interest. Here we present the thermodynamic characterization of structurally distinct inhibitors of the LTA ₄ H that occupy different regions of the binding site using different biophysical methods. An in silico method for the determination of stabilized water molecules in the binding site of the apo structure of LTA ₄ H is used to interpret the measured thermodynamic data and provided insights for design of novel LTA ₄ H inhibitors.

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Organizational Affiliation: 
• Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Street 9, 60438 Frankfurt, Germany. Electronic address: [e-mail].
Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Street 9, 60438 Frankfurt, Germany. Electronic address: [e-mail].
Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Street 9, 60438 Frankfurt, Germany. Electronic address: [e-mail].
Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Street 9, 60438 Frankfurt, Germany. Electronic address: [e-mail].
Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Street 9, 60438 Frankfurt, Germany. Electronic address: [e-mail].
Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Street 9, 60438 Frankfurt, Germany. Electronic address: [e-mail].
Institute of Biochemistry, Goethe University Frankfurt, Max-von-Laue Street 9, 60438 Frankfurt, Germany. Electronic address: [e-mail].
Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Street 9, 60438 Frankfurt, Germany. Electronic address: [e-mail].
Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Project Group Translational Medicine and Pharmacology TMP, Theodor-Stern-Kai 7, D-60596 Frankfurt am Main, Germany. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 73.19 kDa 
• Atom Count: 5,279 
• Modeled Residue Count: 607 
• Deposited Residue Count: 633 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HUMAN LEUKOTRIENE A4 HYDROLASE	A	633	Homo sapiens	Mutation(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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YB	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], L [auth A]	YTTERBIUM (III) ION Yb AWSFICBXMUKWSK-UHFFFAOYSA-N
IMD	I [auth A], J [auth A], K [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.223 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.337	α = 90
b = 86.98	β = 90
c = 96.31	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-05 
Deposition Author(s): Wittmann, S.K., Kalinowsky, L., Kramer, J., Bloecher, R., Steinhilber, D., Pogoryelov, D., Proschak, E., Heering, J.

Revision History  

• Version 1.0: 2016-10-05
  Type: Initial release
  
• Version 1.1: 2016-11-09
  Changes: Database references
• Version 1.2: 2019-05-08
  Changes: Data collection, Database references, Experimental preparation, Other
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description