6DK0

Human sigma-1 receptor bound to NE-100


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.251 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis for sigma1receptor ligand recognition.

Schmidt, H.R.Betz, R.M.Dror, R.O.Kruse, A.C.

(2018) Nat. Struct. Mol. Biol. 25: 981-987


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sigma non-opioid intracellular receptor 1
A, B, C
227Homo sapiensMutation(s): 0 
Gene Names: SIGMAR1 (OPRS1, SRBP)
Find proteins for Q99720 (Homo sapiens)
Go to Gene View: SIGMAR1
Go to UniProtKB:  Q99720
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download SDF File 
Download CCD File 
A, C
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
SO4
Query on SO4

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Download CCD File 
A, B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B, C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
GKY
Query on GKY

Download SDF File 
Download CCD File 
A, B, C
N-{2-[4-methoxy-3-(2-phenylethoxy)phenyl]ethyl}-N-propylpropan-1-amine
C23 H33 N O2
YBLIQJGXRLZBCZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.251 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 85.556α = 90.00
b = 126.062β = 90.00
c = 109.702γ = 90.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (United States)United StatesDGE1745303
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM119185

Revision History 

  • Version 1.0: 2018-10-17
    Type: Initial release