3DL9

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


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 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


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.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cytochrome P450 2R1 AB479Homo sapiensMutation(s): 0 
Gene Names: CYP2R1
EC: 1.14.14 (PDB Primary Data), 1.14.14.24 (UniProt)
Find proteins for Q6VVX0 (Homo sapiens)
Explore Q6VVX0 
Go to UniProtKB:  Q6VVX0
NIH Common Fund Data Resources
PHAROS:  Q6VVX0
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
Cycloheptakis-(1-4)-(alpha-D-glucopyranose)
C, D
7 N/A Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
V2H
Query on V2H

Download Ideal Coordinates CCD File 
A, B
(1S,3R,5Z,7E,22E)-9,10-secoergosta-5,7,10,22-tetraene-1,3-diol
C28 H44 O2
HKXBNHCUPKIYDM-CGMHZMFXSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900012
Query on PRD_900012
C, Dbeta-cyclodextrinOligosaccharide /  Drug delivery

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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 = 137.303α = 90
b = 163.04β = 90
c = 152.588γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-3000data reduction
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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