4HOD | pdb_00004hod

Crystal structure of LeuT-E290S with bound Cl

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.254 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.195 (Depositor) 

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 

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 

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

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transporter515Aquifex aeolicus VF5Mutation(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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO67854
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BOG

Query on BOG


Download:Ideal Coordinates CCD File
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

Query on LEU


Download:Ideal Coordinates CCD File
B [auth A]LEUCINE
C6 H13 N O2
ROHFNLRQFUQHCH-YFKPBYRVSA-N
CL

Query on CL


Download:Ideal Coordinates CCD File
E [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA

Query on NA


Download:Ideal Coordinates CCD File
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), 0.248 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.195 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.58α = 90
b = 87.48β = 95
c = 80.86γ = 90
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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