3V4Z

D-alanine--D-alanine ligase from Yersinia pestis

Structural Biology Knowledgebase: 3V4Z SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.205

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3V4Z

Classification: LIGASE

Total Structure Weight: 67160.90

Macromolecule Entities
Molecule Chains Length Organism Details
D-alanine--D-alanine ligase A, B 309 Yersinia pestis EC#: 6.3.2.4 IUBMB
Gene Name(s): ddl ddlB YPO0557 y3624 YP_3627

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

B TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PEG
Query on PEG

A DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.205
  • Space Group: P 31 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 100.64 α = 90.00
b = 100.64 β = 90.00
c = 110.30 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-12-15
  • Released Date: 2011-12-28
  • Deposition author(s): Osipiuk, J., Nocek, B., Mulligan, R., Papazisi, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History

No revisions since initial release