5OCP

The periplasmic binding protein component of the arabinose ABC transporter from Shewanella sp. ANA-3 bound to alpha and beta-L-arabinofuranose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 3.1 of the entry. See complete history


Literature

CHARACTERISATION OF A FURANOSE SPECIFIC ABC TRANSPORTER ESSENTIAL FOR ARABINOSE UTILISATION FROM THE LIGNOCELLULOSE DEGRADING BACTERIUM SHEWANELLA SP. ANA-3

Herman, R.Drousiotis, K.Wilkinson, A.J.Thomas, G.H.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Periplasmic binding protein/LacI transcriptional regulator
A, B
302Shewanella sp. ANA-3Mutation(s): 0 
Gene Names: Shewana3_2073
UniProt
Find proteins for A0KWY4 (Shewanella sp. (strain ANA-3))
Explore A0KWY4 
Go to UniProtKB:  A0KWY4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0KWY4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AHR (Subject of Investigation/LOI)
Query on AHR

Download Ideal Coordinates CCD File 
I [auth A],
N [auth B]
alpha-L-arabinofuranose
C5 H10 O5
HMFHBZSHGGEWLO-QMKXCQHVSA-N
FUB (Subject of Investigation/LOI)
Query on FUB

Download Ideal Coordinates CCD File 
J [auth A],
O [auth B]
beta-L-arabinofuranose
C5 H10 O5
HMFHBZSHGGEWLO-KLVWXMOXSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
K [auth B],
L [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
M [auth B]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.917α = 90
b = 86.327β = 90
c = 87.282γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2018-08-01 
  • Deposition Author(s): Herman, R.

Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/N01040X/1

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 2.0: 2018-12-19
    Changes: Atomic model, Data collection, Derived calculations
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 3.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary