2YZM

Structure of D-Alanine:D-Alanine Ligase with substrate from Thermus thermophilus HB8

Structural Biology Knowledgebase: 2YZM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.224

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2YZM

Classification: Ligase

Total Structure Weight: 104367.88

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

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DAL
Query on DAL

A, B, C 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: 2.21 Å
  • R-Value Free: 0.266
  • R-Value Work: 0.224
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 166.71 α = 90.00
b = 55.85 β = 109.34
c = 141.39 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-05-06
  • Released Date: 2007-11-06
  • Deposition author(s): Kitamura, 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
  • 2011-07-13
    Type: Source and taxonomy | Details: Removed strain from scientific name