1W1D

CRYSTAL STRUCTURE OF THE PDK1 PLECKSTRIN HOMOLOGY (PH) DOMAIN BOUND TO INOSITOL (1,3,4,5)-TETRAKISPHOSPHATE

Structural Biology Knowledgebase: 1W1D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.200
  • R-Value Work: 0.145

Literature

Macromolecules
Sequence Display for 1W1D

Classification: TRANSFERASE

Total Structure Weight: 18605.49

Macromolecule Entities
Molecule Chains Length Organism Details
3-PHOSPHOINOSITIDE DEPENDENT PROTEIN KINASE-1 A 151 Homo sapiens EC#: 2.7.11.1 IUBMB
Fragment: PLECKSTRIN HOMOLOGY DOMAIN, RESIDUES 409-556
Gene Name(s): PDPK1 Gene View PDK1 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
4IP
Query on 4IP

A INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE
C6 H16 O18 P4
CIPFCGZLFXVXBG-CNWJWELYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
AU
Query on AU

A GOLD ION
Au
ZBKIUFWVEIBQRT-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
4IP N/A in BindingDB
Ki: 300 nM  BindingMOAD
Ki: 300 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.200
  • R-Value Work: 0.145
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 35.40 α = 90.00
b = 58.92 β = 101.48
c = 36.58 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-06-21
  • Released Date: 2004-11-19
  • Deposition author(s): Komander, D., Deak, M., Alessi, D.R., Van Aalten, D.M.F.

Revision History

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