3DL9

Crystal structure of CYP2R1 in complex with 1-alpha-hydroxy-vitamin D2

• PDB DOI: https://doi.org/10.2210/pdb3DL9/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-06-26 Released: 2008-08-05 
• Deposition Author(s): Strushkevich, N.V., Tempel, W., Gilep, A.A., Loppnau, P., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Wilkstrom, M., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free: 0.218 
• R-Value Work: 0.183 
• R-Value Observed: 0.184 

Starting Model: experimental

Literature

Crystal structure of CYP2R1 in complex with 1-alpha-hydroxy-vitamin D2.

Strushkevich, N.V., Tempel, W., Gilep, A.A., Loppnau, P., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Wilkstrom, M., Bochkarev, A., Park, H.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 114.65 kDa 
• Atom Count: 7,959 
• Modelled Residue Count: 932 
• Deposited Residue Count: 958 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome P450 2R1	A, B	479	Homo sapiens	Mutation(s): 0  Gene Names: CYP2R1 EC: 1.14.14
UniProt & NIH Common Fund Data Resources
Find proteins for Q6VVX0 (Homo sapiens) Explore Q6VVX0  Go to UniProtKB:  Q6VVX0
GTEx:  ENSG00000186104

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
Cycloheptakis-(1-4)-(alpha-D-glucopyranose)	C, D	7		N/A
Glycosylation Resources
GlyTouCan:  G01435GL GlyCosmos:  G01435GL

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	E [auth A], G [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
V2H	F [auth A], H [auth B]	(1S,3R,5Z,7E,22E)-9,10-secoergosta-5,7,10,22-tetraene-1,3-diol C28 H44 O2 HKXBNHCUPKIYDM-CGMHZMFXSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900012	C, D	beta-cyclodextrin	Oligosaccharide / Drug delivery

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.72 Å
• R-Value Free: 0.218 
• R-Value Work: 0.183 
• R-Value Observed: 0.184 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.303	α = 90
b = 163.04	β = 90
c = 152.588	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-3000	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-08-05 
Deposition Author(s): Strushkevich, N.V., Tempel, W., Gilep, A.A., Loppnau, P., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Wilkstrom, M., Bochkarev, A., Park, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-08-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-08-30
  Changes: Data collection, Database references, Refinement description, Structure summary