4MIJ

Crystal structure of a Trap periplasmic solute binding protein from Polaromonas sp. JS666 (Bpro_3107), target EFI-510173, with bound alpha/beta D-Galacturonate, space group P21

Structural Biology Knowledgebase: 4MIJ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.152
  • R-Value Work: 0.138

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4MIJ

Classification: TRANSPORT PROTEIN

Total Structure Weight: 37208.21

Macromolecule Entities
Molecule Chains Length Organism Details
TRAP dicarboxylate transporter, DctP subunit A 337 Polaromonas sp. js666 Gene Name(s): Bpro_3107

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

A ALPHA-D-GALACTOPYRANURONIC ACID
ALPHA D-GALACTURONIC ACID (Synonym)
C6 H10 O7
AEMOLEFTQBMNLQ-BKBMJHBISA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GTR
Query on GTR

A Beta-D-Galactopyranuronic acid
Galacturonic acid (Synonym)
C6 H10 O7
AEMOLEFTQBMNLQ-DTEWXJGMSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.152
  • R-Value Work: 0.138
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 45.53 α = 90.00
b = 46.14 β = 97.56
c = 63.90 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-08-31
  • Released Date: 2013-09-18
  • Deposition author(s): Vetting, M.W., Toro, R., Bhosle, R., Al Obaidi, N.F., Morisco, L.L., Wasserman, S.R., Sojitra, S., Zhao, S., Stead, M., Washington, E., Scott Glenn, A., Chowdhury, S., Evans, B., Hammonds, J., Hillerich, B., Love, J., Seidel, R.D., Imker, H.J., Jacobson, M.P., Gerlt, J.A., Almo, S.C., Enzyme Function Initiative (EFI)

Revision History

  • 2015-10-14
    Type: Non-polymer description | Details: update ligand name
  • 2015-02-25
    Type: Citation | Details: Citation update