2ZDQ

Crystal structure of D-Alanine:D-Alanine Ligase with ATP and D-Alanine:D-Alanine from Thermus thermophius HB8

Structural Biology Knowledgebase: 2ZDQ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.231

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2ZDQ

Classification: Ligase

Total Structure Weight: 70771.14

Macromolecule Entities
Molecule Chains Length Organism Details
D-alanine--D-alanine ligase A, B 319 Thermus thermophilus EC#: 6.3.2.4 IUBMB
Gene Name(s): ddl TTHA1587

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

A, B ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DAL
Query on DAL

A, B D-ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-UWTATZPHSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.231
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 95.05 α = 90.00
b = 95.05 β = 90.00
c = 192.01 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-11-27
  • Released Date: 2008-05-27
  • Deposition author(s): Kitamuta, Y., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4