2QV7

Crystal Structure of Diacylglycerol Kinase DgkB in complex with ADP and Mg

Structural Biology Knowledgebase: 2QV7 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.246
  • R-Value Work: 0.206

Literature

Macromolecules
Sequence Display for 2QV7

Classification: TRANSFERASE

Total Structure Weight: 38351.16

Macromolecule Entities
Molecule Chains Length Organism Details
Diacylglycerol Kinase DgkB A 337 Staphylococcus aureus EC#: 2.7.1.107 IUBMB
Gene Name(s): dagK dgkB SAR1989
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
ADP N/A in BindingDB
N/A in BindingMoad
Kd: 219000 nM  PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.246
  • R-Value Work: 0.206
  • Space Group: P 42 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 123.76 α = 90.00
b = 123.76 β = 90.00
c = 47.68 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-08-07
  • Released Date: 2008-06-17
  • Deposition author(s): Miller, D.J., Jerga, A., Rock, C.O., White, S.W.

Revision History

  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Refinement description | Details: Fixed TLS group
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4