3IC1

Crystal structure of zinc-bound succinyl-diaminopimelate desuccinylase from Haemophilus influenzae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.194

Literature

Macromolecules
Sequence Display for 3IC1

Classification: HYDROLASE

Total Structure Weight: 83722.70

Macromolecule Entities
Molecule Chains Length Organism Details
Succinyl-diaminopimelate desuccinylase A, B 377 Haemophilus influenzae EC#: 3.5.1.18 IUBMB
Gene Name(s): dapE HI_0102
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-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: 2.3 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.194
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 44.70 α = 90.00
b = 95.75 β = 90.00
c = 185.43 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-07-17
  • Released Date: 2009-09-22
  • Deposition author(s): Nocek, B.P., Gillner, D.M., Holz, R.C., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update