4CK0

Crystal structure of the integral membrane diacylglycerol kinase - form 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.924 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.248 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of the Integral Membrane Diacylglycerol Kinase with Zn-Amppcp Bound and its Catalytic Mechanism

Li, D.Caffrey, M.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIACYLGLYCEROL KINASE
A, B, C
130Escherichia coli (strain K12)Mutation(s): 4 
Gene Names: dgkA
EC: 2.7.1.107
Find proteins for P0ABN1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ABN1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

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Download CCD File 
B
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACP
Query on ACP

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Download CCD File 
C
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.924 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.248 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 72.820α = 90.00
b = 72.820β = 90.00
c = 195.670γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2016-11-16
    Type: Database references
  • Version 1.2: 2019-03-06
    Type: Data collection, Experimental preparation, Other
  • Version 1.3: 2019-04-03
    Type: Data collection, Experimental preparation