5C0P

The crystal structure of endo-arabinase from Bacteroides thetaiotaomicron VPI-5482


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.164
  • R-Value Work: 0.149

Literature

Macromolecules
Sequence Display for 5C0P

Classification: HYDROLASE

Total Structure Weight: 34328.13

Macromolecule Entities
Molecule Chains Length Organism Details
Endo-arabinase A 298 Bacteroides thetaiotaomicron Gene Name(s): BT_1873
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
TRS
Query on TRS

A 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER (Synonym)
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.164
  • R-Value Work: 0.149
  • Space Group: P 43

Unit Cell:

Length (Å) Angle (°)
a = 83.80 α = 90.00
b = 83.80 β = 90.00
c = 43.37 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2015-06-12
  • Released Date: 2015-07-01
  • Deposition author(s): Tan, K., Cuff, M., Joachimiak, G., Endres, M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History

  • Version 1_0: 2015-07-01

    Type: Initial release

  • Version 1_1: 2017-09-27

    Type: Advisory, Author supporting evidence, Derived calculations, Source and taxonomy, Structure summary