2QJU

Crystal Structure of an NSS Homolog with Bound Antidepressant

• PDB DOI: https://doi.org/10.2210/pdb2QJU/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Aquifex aeolicus VF5
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2007-07-09 Released: 2007-08-21 
• Deposition Author(s): Zhou, Z., Karpowich, N.K., Wang, D.N., New York Consortium on Membrane Protein Structure (NYCOMPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.220 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 58.77 kDa 
• Atom Count: 4,172 
• Modelled Residue Count: 509 
• Deposited Residue Count: 511 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transporter	A	511	Aquifex aeolicus VF5	Mutation(s): 0  Gene Names: snf Membrane Entity: Yes
UniProt
Find proteins for O67854 (Aquifex aeolicus (strain VF5)) Explore O67854  Go to UniProtKB:  O67854

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BOG	B [auth A], C [auth A], D [auth A], E [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
DSM	J [auth A]	3-(10,11-DIHYDRO-5H-DIBENZO[B,F]AZEPIN-5-YL)-N-METHYLPROPAN-1-AMINE C18 H22 N2 HCYAFALTSJYZDH-UHFFFAOYSA-N
LEU	I [auth A]	LEUCINE C6 H13 N O2 ROHFNLRQFUQHCH-YFKPBYRVSA-N
CL	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	F [auth A], G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
DSM	PDBBind:  2QJU	IC50: 8.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.220 
• R-Value Work: 0.199 
• R-Value Observed: 0.199 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.414	α = 90
b = 86.763	β = 95.72
c = 81.187	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-21 
Deposition Author(s): Zhou, Z., Karpowich, N.K., Wang, D.N., New York Consortium on Membrane Protein Structure (NYCOMPS)

Revision History  

• Version 1.0: 2007-08-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Refinement description, Structure summary