4M48

X-ray structure of dopamine transporter elucidates antidepressant mechanism

Structural Biology Knowledgebase: 4M48 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.221

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4M48

Classification: TRANSPORT PROTEIN

Total Structure Weight: 113434.08

Macromolecule Entities
Molecule Chains Length Organism Details
Transporter A 543 Drosophila melanogaster Fragment: SEE REMARK 999
Mutation: V74A, V275A, V311A, L415A, G538L
Gene Name(s): DAT fmn CG8380
9D5 antibody, light chain L 237 Mus musculus Fragment: Fab, papain cleavage fragment
9D5 antibody, heavy chain H 240 Mus musculus Fragment: Fab, papain cleavage fragment

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Solute Carrier (SLC) Transporter Superfamily

Protein Name: DAT Dopamine transporter in complex with nortriptyline TCA (tricyclic antidepressant)


Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
CLR
Query on CLR

A CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
21B
Query on 21B

A Nortriptyline
3-(10,11-dihydro-5H-dibenzo[a,d][7]annulen- 5-ylidene)-N-methylpropan-1-amine (Synonym)
C19 H21 N
PHVGLTMQBUFIQQ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
21B N/A in BindingDB
N/A in BindingMoad
Ki: 156 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.221
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 97.84 α = 90.00
b = 133.68 β = 90.00
c = 162.44 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-08-06
  • Released Date: 2013-09-18
  • Deposition author(s): Gouaux, E., Penmatsa, A., Wang, K.

Revision History

  • 2013-11-13
    Type: Citation | Details: Citation update
  • 2013-10-09
    Type: Biological assembly | Details: corrected quaternary structure
  • 2013-10-02
    Type: Citation | Details: Citation update