3DHV

Crystal structure of DltA protein in complex with D-alanine adenylate

Structural Biology Knowledgebase: 3DHV SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.213

Literature

Macromolecules
Sequence Display for 3DHV

Classification: LIGASE

Total Structure Weight: 58002.55

Macromolecule Entities
Molecule Chains Length Organism Details
D-alanine-poly(phosphoribitol) ligase A 512 Bacillus cereus EC#: 6.1.1.13 IUBMB
Mutation: M1A
Gene Name(s): dltA BC_1372
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DAL
Query on DAL

A D-ALANINE
C3 H7 N O2
QNAYBMKLOCPYGJ-UWTATZPHSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
DAL N/A in BindingDB
N/A in BindingMoad
Kd: 1100000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.252
  • R-Value Work: 0.213
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 60.70 α = 90.00
b = 86.70 β = 113.50
c = 57.40 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-06-18
  • Released Date: 2008-11-04
  • Deposition author(s): Du, L., He, Y., Luo, Y.

Revision History

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