Macromolecule Content

Total Structure Weight: 71.21 kDa
Atom Count: 5907
Residue Count: 608
Unique protein chains: 1

3U9W

Structure of human Leukotriene A4 hydrolase in complex with inhibitor sc57461A

DOI: 10.2210/pdb3U9W/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-10-20 Released: 2012-10-24
Deposition Author(s): Niegowski, D., Thunnissen, M., Tholander, F., Rinaldo-Matthis, A., Muroya, A., Haeggstrom, J.Z.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.161
R-Value Work: 0.134
R-Value Observed: 0.134

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structure of human Leukotriene A4 hydrolase in complex with inhibitor sc57461A

Olsson, U., Niegowski, D., Stsiapanava, A., Thunnissen, M., Haeggstrom, J.Z., Rinaldo-Matthis, A.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leukotriene A-4 hydrolase	A	608	Homo sapiens	Mutation(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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
28P Query on 28P Download Ideal Coordinates CCD File SDF format, chain I [A] MOL2 format, chain I [A]	A	N-[3-(4-benzylphenoxy)propyl]-N-methyl-beta-alanine C₂₀ H₂₅ N O₃ HSXNVULMYZGNGF-UHFFFAOYSA-N		Ligand Interaction
YB Query on YB Download Ideal Coordinates CCD File SDF format, chain C [A] SDF format, chain K [A] SDF format, chain L [A] SDF format, chain M [A] SDF format, chain N [A] SDF format, chain O [A] SDF format, chain P [A] SDF format, chain Q [A] MOL2 format, chain C [A] MOL2 format, chain K [A] MOL2 format, chain L [A] MOL2 format, chain M [A] MOL2 format, chain N [A] MOL2 format, chain O [A] MOL2 format, chain P [A] MOL2 format, chain Q [A]	A	YTTERBIUM (III) ION Yb AWSFICBXMUKWSK-UHFFFAOYSA-N		Ligand Interaction
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [A] MOL2 format, chain H [A]	A	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Ligand Interaction
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain F [A] SDF format, chain G [A] SDF format, chain R [A] MOL2 format, chain F [A] MOL2 format, chain G [A] MOL2 format, chain R [A]	A	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Ligand Interaction
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [A] MOL2 format, chain B [A]	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain J [A] MOL2 format, chain J [A]	A	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Ligand Interaction
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain D [A] SDF format, chain E [A] MOL2 format, chain D [A] MOL2 format, chain E [A]	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
28P	Kd: 60 nM BindingDB
28P	IC50: 2.5 nM BindingDB
28P	Kd: 290 nM BindingDB
28P	Ki: 3 nM BindingDB
28P	Kd: 350 nM BindingDB
28P	IC50: 6 nM BindingDB
28P	IC50: 49 nM BindingDB

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.161
R-Value Work: 0.134
R-Value Observed: 0.134
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.078	α = 90
b = 86.799	β = 90
c = 99.145	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
AUTOMAR	data collection

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2011-10-20
Released Date: 2012-10-24

Deposition Author(s):

Rinaldo-Matthis, A.

Haeggstrom, J.Z.

Revision History

Version 1.0: 2012-10-24
Type: Initial release
Version 1.1: 2018-03-07
Changes: Data collection

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.