3V2W

Crystal Structure of a Lipid G protein-Coupled Receptor at 3.35A

Structural Biology Knowledgebase: 3V2W SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.281
  • R-Value Work: 0.224

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3V2W

Classification: HYDROLASE

Total Structure Weight: 59537.38

Macromolecule Entities
Molecule Chains Length Organism Details
Sphingosine 1-phosphate receptor 1, Lysozyme chimera A 520 Homo sapiens Enterobacteria phage t4 sensu lato EC#: 3.2.1.17 IUBMB
Mutation: C1054T, C1097A, ΔK250, S251N, L252V
Gene Name(s): E S1PR1 Gene View CHEDG1 EDG1

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: G Protein-Coupled Receptors (GPCRs)

Protein Name: Sphingosine 1-phosphate receptor


Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ML5
Query on ML5

A {(3R)-3-amino-4-[(3-hexylphenyl)amino]-4- oxobutyl}phosphonic acid
C16 H27 N2 O4 P
FWJRVGZWNDOOFH-OAHLLOKOSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
ML5 N/A in BindingDB
N/A in BindingMoad
Ki: 77 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.281
  • R-Value Work: 0.224
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 107.94 α = 90.00
b = 69.70 β = 90.00
c = 81.93 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-12-12
  • Released Date: 2012-02-15
  • Deposition author(s): Hanson, M.A., Roth, C.B., Jo, E., Griffith, M.T., Scott, F.L., Reinhart, G., Desale, H., Clemons, B., Cahalan, S.M., Schuerer, S.C., Sanna, M.G., Han, G.W., Kuhn, P., Rosen, H., Stevens, R.C., GPCR Network (GPCR)

Revision History

  • 2012-03-14
    Type: Citation | Details: Citation update