5UPH

Lipids bound lysosomal integral membrane protein 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Lysosomal integral membrane protein-2 as a phospholipid receptor revealed by biophysical and cellular studies.

Conrad, K.S.Cheng, T.W.Ysselstein, D.Heybrock, S.Hoth, L.R.Chrunyk, B.A.Am Ende, C.W.Krainc, D.Schwake, M.Saftig, P.Liu, S.Qiu, X.Ehlers, M.D.

(2017) Nat Commun 8: 1908-1908


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysosome membrane protein 2
A, B
410Homo sapiensMutation(s): 0 
Gene Names: SCARB2 (CD36L2, LIMP2, LIMPII)
Find proteins for Q14108 (Homo sapiens)
Go to Gene View: SCARB2
Go to UniProtKB:  Q14108
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
M6D
Query on M6D

Download SDF File 
Download CCD File 
A
6-O-phosphono-beta-D-mannopyranose
beta-D-mannose-6-phosphate
C6 H13 O9 P
NBSCHQHZLSJFNQ-RWOPYEJCSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, B
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
PCW
Query on PCW

Download SDF File 
Download CCD File 
A, B
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
(Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE
C44 H85 N O8 P
SNKAWJBJQDLSFF-NVKMUCNASA-O
 Ligand Interaction
CLR
Query on CLR

Download SDF File 
Download CCD File 
A, B
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.193 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 139.040α = 90.00
b = 139.040β = 90.00
c = 178.280γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
PHASERphasing
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-02-03 
  • Released Date: 2017-12-13 
  • Deposition Author(s): Conrad, K.S., Liu, S.

Revision History 

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2018-12-26
    Type: Data collection, Database references