4HOD | pdb_00004hod

Crystal structure of LeuT-E290S with bound Cl

• PDB DOI: https://doi.org/10.2210/pdb4HOD/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Aquifex aeolicus VF5
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2012-10-22 Released: 2013-05-08 
• Deposition Author(s): Kantcheva, A.K., Quick, M., Shi, L., Winther, A.M.L., Stolzenberg, S., Weinstein, H., Javitch, J.A., Nissen, P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free: 
  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Literature

The chloride binding site of Neurotransmitter Sodium Symporters

Kantcheva, A.K., Quick, M., Shi, L., Winther, A.M.L., Stolzenberg, S., Weinstein, H., Javitch, J.A., Nissen, P.

(2013) Proc Natl Acad Sci U S A 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 59.24 kDa 
• Atom Count: 4,153 
• Modeled Residue Count: 509 
• Deposited Residue Count: 515 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transporter	A	515	Aquifex aeolicus VF5	Mutation(s): 1  Gene Names: snf, aq_2077 Membrane Entity: Yes
UniProt
Find proteins for O67854 (Aquifex aeolicus (strain VF5)) Explore O67854  Go to UniProtKB:  O67854

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BOG	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
LEU	B [auth A]	LEUCINE C6 H13 N O2 ROHFNLRQFUQHCH-YFKPBYRVSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A], D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.30 Å
• R-Value Free:  0.254 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.58	α = 90
b = 87.48	β = 95
c = 80.86	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-08 
Deposition Author(s): Kantcheva, A.K., Quick, M., Shi, L., Winther, A.M.L., Stolzenberg, S., Weinstein, H., Javitch, J.A., Nissen, P.

Revision History  

• Version 1.0: 2013-05-08
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Data collection, Refinement description
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Structure summary