4XP9

X-ray structure of Drosophila dopamine transporter bound to psychostimulant D-amphetamine

• PDB DOI: https://doi.org/10.2210/pdb4XP9/pdb

• Classification: transport protein/inhibitor
• Organism(s): Drosophila melanogaster, Mus musculus
• Expression System: Homo sapiens, Mus musculus
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2015-01-16 Released: 2015-05-06 
• Deposition Author(s): Aravind, P., Wang, K., Gouaux, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.242 
• R-Value Work: 0.211 
• R-Value Observed: 0.212 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 109.73 kDa 
• Atom Count: 7,665 
• Modelled Residue Count: 969 
• Deposited Residue Count: 973 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transporter	A [auth C]	541	Drosophila melanogaster	Mutation(s): 2  Gene Names: DAT, CG8380, Dmel_CG8380 Membrane Entity: Yes
UniProt
Find proteins for Q7K4Y6 (Drosophila melanogaster) Explore Q7K4Y6  Go to UniProtKB:  Q7K4Y6

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ANTIBODY FRAGMENT HEAVY CHAIN-PROTEIN, 9D5-HEAVY CHAIN	B [auth L]	213	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ANTIBODY FRAGMENT LIGHT CHAIN-PROTEIN, 9D5-LIGHT CHAIN	C [auth H]	219	Mus musculus	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	D [auth A]	2		N/A
Glycosylation Resources
GlyTouCan:  G07411ON GlyCosmos:  G07411ON

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y01	E [auth C]	CHOLESTEROL HEMISUCCINATE C31 H50 O4 WLNARFZDISHUGS-MIXBDBMTSA-N
CLR	H [auth C]	CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N
NAG	F [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MPO	G [auth C]	3[N-MORPHOLINO]PROPANE SULFONIC ACID C7 H15 N O4 S DVLFYONBTKHTER-UHFFFAOYSA-N
P4G	J [auth C], K [auth C]	1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE C8 H18 O3 RRQYJINTUHWNHW-UHFFFAOYSA-N
1WE	I [auth C]	(2S)-1-phenylpropan-2-amine C9 H13 N KWTSXDURSIMDCE-QMMMGPOBSA-N
CL	N [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	L [auth C], M [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	D [auth A]	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.242 
• R-Value Work: 0.211 
• R-Value Observed: 0.212 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.348	α = 90
b = 140.748	β = 90
c = 166.76	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-06 
Deposition Author(s): Aravind, P., Wang, K., Gouaux, E.

Revision History  

• Version 1.0: 2015-05-06
  Type: Initial release
  
• Version 1.1: 2015-05-27
  Changes: Database references
• Version 1.2: 2015-06-03
  Changes: Database references
• Version 1.3: 2015-11-25
  Changes: Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary