4PR7

KdgM porin in complex with disordered oligogalacturonate

Structural Biology Knowledgebase: 4PR7 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.208

Literature

Macromolecules
Sequence Display for 4PR7

Classification: OUTER MEMBRANE PROTEIN

Total Structure Weight: 27514.67

Macromolecule Entities
Molecule Chains Length Organism Details
Oligogalacturonate-specific porin KdgM A 222 Dickeya dadantii Fragment: UNP residues 21-236
Gene Name(s): kdgM Dda3937_03362
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: BETA-BARREL

Subgroup Name: Beta-Barrel Membrane Proteins: Porins and Relatives

Protein Name: KdgM *monomeric* porin in complex with disordered oligogalacturonate


Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
C8E
Query on C8E

A (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
C16 H34 O5
FEOZZFHAVXYAMB-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ADA
Query on ADA

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

A N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.245
  • R-Value Work: 0.208
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 36.86 α = 90.00
b = 59.73 β = 106.54
c = 51.60 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2014-03-05
  • Released Date: 2014-06-11
  • Deposition author(s): Hutter, C., Peneff, C.M., Wirth, C., Schirmer, T.

Revision History

  • 2014-09-24
    Type: Citation | Details: Citation update