3B6H

Crystal structure of human prostacyclin synthase in complex with inhibitor minoxidil

• PDB DOI: https://doi.org/10.2210/pdb3B6H/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2007-10-29 Released: 2007-11-20 
• Deposition Author(s): Li, Y.-C., Chiang, C.-W., Yeh, H.-C., Hsu, P.-Y., Whitby, F.G., Wang, L.-H., Chan, N.-L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.228 
• R-Value Work: 0.203 
• R-Value Observed: 0.204 

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 116.78 kDa 
• Atom Count: 8,552 
• Modelled Residue Count: 939 
• Deposited Residue Count: 996 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prostacyclin synthase	A, B	498	Homo sapiens	Mutation(s): 0  Gene Names: PTGIS, CYP8, CYP8A1 EC: 5.3.99.4 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q16647 (Homo sapiens) Explore Q16647  Go to UniProtKB:  Q16647
PHAROS:  Q16647 GTEx:  ENSG00000124212

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A], H [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
BOG	C [auth A], F [auth B]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
MXD	D [auth A], G [auth B]	6-PIPERIDIN-1-YLPYRIMIDINE-2,4-DIAMINE 3-OXIDE C9 H15 N5 O ZFMITUMMTDLWHR-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
MXD	Binding MOAD:  3B6H	Kd: 3400 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.228 
• R-Value Work: 0.203 
• R-Value Observed: 0.204 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.762	α = 90
b = 106.072	β = 91.81
c = 73.901	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-11-20 
Deposition Author(s): Li, Y.-C., Chiang, C.-W., Yeh, H.-C., Hsu, P.-Y., Whitby, F.G., Wang, L.-H., Chan, N.-L.

Revision History  

• Version 1.0: 2007-11-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary