1DJX

PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C-DELTA1 FROM RAT COMPLEXED WITH INOSITOL-1,4,5-TRISPHOSPHATE

Structural Biology Knowledgebase: 1DJX SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.270
  • R-Value Work: 0.220

Literature

Macromolecules
Sequence Display for 1DJX

Classification: LIPID DEGRADATION

Total Structure Weight: 142268.91

Macromolecule Entities
Molecule Chains Length Organism Details
PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C, ISOZYME DELTA1 A, B 624 Rattus norvegicus EC#: 3.1.4.11 IUBMB
Details: CATALYTICALLY-ACTIVE DELETION VARIANT THAT LACKS AN N-TERMINAL PH DOMAIN, COMPLEXED WITH INOSITOL-1,4,5-TRISPHOSPHATE
Gene Name(s): Plcd1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
I3P
Query on I3P

A, B D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE
C6 H15 O15 P3
MMWCIQZXVOZEGG-XJTPDSDZSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ACT
Query on ACT

A, B ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
I3P N/A in BindingDB
Kd: 1700 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.270
  • R-Value Work: 0.220
  • Space Group: F 41 3 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 397.54 α = 90.00
b = 397.54 β = 90.00
c = 397.54 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1996-08-24
  • Released Date: 1997-07-07
  • Deposition author(s): Essen, L.-O., Perisic, O., Williams, R.L.

Revision History

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