3O19 | pdb_00003o19

Structure-function analysis of human L-Prostaglandin D Synthase bound with fatty acid

• PDB DOI: https://doi.org/10.2210/pdb3O19/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-07-21 Released: 2010-09-22 
• Deposition Author(s): Zhou, Y., Shaw, N., Li, Y., Zhao, Y., Zhang, R., Liu, Z.-J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free: 
  0.244 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Structure-function analysis of human L-Prostaglandin D Synthase bound with fatty acid

Zhou, Y., Shaw, N., Li, Y., Zhao, Y., Zhang, R., Liu, Z.-J.

To be published.

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: 18.63 kDa 
• Atom Count: 1,451 
• Modeled Residue Count: 154 
• Deposited Residue Count: 162 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prostaglandin-H2 D-isomerase	A	162	Homo sapiens	Mutation(s): 1  Gene Names: PTGDS, PDS EC: 5.3.99.2
UniProt & NIH Common Fund Data Resources
Find proteins for P41222 (Homo sapiens) Explore P41222  Go to UniProtKB:  P41222
PHAROS:  P41222 GTEx:  ENSG00000107317

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OLA	B [auth A]	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
PLM	C [auth A]	PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.66 Å
• R-Value Free:  0.244 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.512	α = 90
b = 60.512	β = 90
c = 177.23	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
CNS	refinement
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-22 
Deposition Author(s): Zhou, Y., Shaw, N., Li, Y., Zhao, Y., Zhang, R., Liu, Z.-J.

Revision History  

• Version 1.0: 2010-09-22
  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
• Version 1.3: 2024-11-20
  Changes: Structure summary