1DJW

PHOSPHOINOSITIDE-SPECIFIC PHOSPHOLIPASE C-DELTA1 FROM RAT COMPLEXED WITH INOSITOL-2-METHYLENE-1,2-CYCLIC-MONOPHOSPHONATE

Structural Biology Knowledgebase: 1DJW SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.270
  • R-Value Work: 0.217

Literature

Macromolecules
Sequence Display for 1DJW

Classification: LIPID DEGRADATION

Total Structure Weight: 141989.16

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-2-METHYLENE-1,2-CYCLIC-MONOPHOSPHONATE
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
CIP
Query on CIP

A, B INOSITOL-2-METHYLENE-1,2-CYCLIC-MONOPHOSPHATE
C7 H13 O7 P
HSPMBPCIFXNUBY-YXVPSNDASA-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)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.270
  • R-Value Work: 0.217
  • Space Group: F 41 3 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 397.03 α = 90.00
b = 397.03 β = 90.00
c = 397.03 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1996-08-24
  • Released Date: 1997-07-23
  • 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