3ZE3

Crystal structure of the integral membrane diacylglycerol kinase - delta7

Structural Biology Knowledgebase: 3ZE3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.217
  • R-Value Work: 0.196

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3ZE3

Classification: TRANSFERASE

Total Structure Weight: 89675.01

Macromolecule Entities
Molecule Chains Length Organism Details
DIACYLGLYCEROL KINASE A, B, C..., D, E, FA, B, C, D, E, F 130 Escherichia coli EC#: 2.7.1.107 IUBMB
Mutation: A41C, C46A, I53V, I70L, M96L, V107D, C113A
Gene Name(s): dgkA b4042 JW4002
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Phosphotransferases

Protein Name: DgkA diacylglycerol kinase (DAGK)


Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
78M
Query on 78M

A, D (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
7.8 MONOACYLGLYCEROL (Synonym)
C18 H34 O4
BJMLBVHMHXYQFS-JJEJIETFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
78N
Query on 78N

A, B, C (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
7.8 MONOACYLGLYCEROL (2R) (Synonym)
C18 H34 O4
BJMLBVHMHXYQFS-XZVRFQMRSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FLC
Query on FLC

D CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

D ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

D ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

E, F SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.217
  • R-Value Work: 0.196
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 75.06 α = 90.00
b = 91.54 β = 90.00
c = 143.65 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-12-03
  • Released Date: 2013-05-22
  • Deposition author(s): Li, D., Pye, V.E., Lyons, J.A., Vogeley, L., Aragao, D., Caffrey, M.

Revision History

  • 2013-06-05
    Type: Citation | Details: JRNL
  • 2013-05-29
    Type: Citation | Details: JRNL