3HKK | pdb_00003hkk

Structure of human Leukotriene C4 synthase in complex with glutathione sulfonate

• PDB DOI: https://doi.org/10.2210/pdb3HKK/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2009-05-24 Released: 2010-05-26 
• Deposition Author(s): Rinaldo-Matthis, A., Haeggstrom, J.Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Pre-steady state kinetics of human Leukotriene C4 synthase

Rinaldo-Matthis, A., Wetterholm, A., Holm, J., Ohlsson, E., Tibbelin, G., Morgenstern, R., Haeggstrom, J.Z.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 19.56 kDa 
• Atom Count: 1,284 
• Modeled Residue Count: 145 
• Deposited Residue Count: 156 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Leukotriene C4 synthase	A	156	Homo sapiens	Mutation(s): 0  EC: 4.4.1.20 (PDB Primary Data), 2.5.1 (UniProt) Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q16873 (Homo sapiens) Explore Q16873  Go to UniProtKB:  Q16873
PHAROS:  Q16873

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTS	H [auth A]	GLUTATHIONE SULFONIC ACID C10 H17 N3 O9 S QGWRMTHFAZVWAM-WDSKDSINSA-N
PLM	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], I [auth A]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N
PAM	B [auth A]	PALMITOLEIC ACID C16 H30 O2 SECPZKHBENQXJG-FPLPWBNLSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: F 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 170.718	α = 90
b = 170.718	β = 90
c = 170.718	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PXSOFT	data collection
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-26 
Deposition Author(s): Rinaldo-Matthis, A., Haeggstrom, J.Z.

Revision History  

• Version 1.0: 2010-05-26
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description