4BPA

Crystal structure of AmpDh2 from Pseudomonas aeruginosa in complex with NAG-NAM-NAG-NAM tetrasaccharide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.290
  • R-Value Work: 0.223

Literature

Macromolecules
Sequence Display for 4BPA

Classification: HYDROLASE

Total Structure Weight: 59005.34

Macromolecule Entities
Molecule Chains Length Organism Details
AMPDH2 A, B 259 Pseudomonas aeruginosa Gene Name(s): ampDh2 PA5485
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

B METHYL 2-(ACETYLAMINO)-3-O-[(1R)-1-CARBOXYETHYL]- 2-DEOXY-BETA-D-GLUCOPYRANOSIDE
C12 H21 N O8
UXEQYDNCHCKBIL-PKKPQKKZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
AMU
Query on AMU

B BETA-N-ACETYLMURAMIC ACID
C11 H19 N O8
MNLRQHMNZILYPY-YVNCZSHWSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

B N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.290
  • R-Value Work: 0.223
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 45.23 α = 90.00
b = 93.56 β = 90.00
c = 104.35 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-05-23
  • Released Date: 2013-07-17
  • Deposition author(s): Artola-Recolons, C., Martinez-Caballero, S., Lee, M., Carrasco-Lopez, C., Hesek, D., Spink, E., Lastochkin, E., Zhang, W., Hellman, L., Boggess, B., Mobashery, S., Hermoso, J.A.

Revision History

  • Version 1_0: 2013-07-17

    Type: Initial release

  • Version 1_1: 2013-07-31

    Type: Database references