2VKI

STRUCTURE OF THE PDK1 PH DOMAIN K465E MUTANT

Structural Biology Knowledgebase: 2VKI SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.215
  • R-Value Work: 0.173

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2VKI

Classification: TRANSFERASE

Total Structure Weight: 17737.15

Macromolecule Entities
Molecule Chains Length Organism Details
3-PHOPSHOINOSITIDE DEPENDENT PROTEIN KINASE 1 A 148 Homo sapiens EC#: 2.7.11.1 IUBMB
Fragment: PLECKSTRIN HOMOLOGY (PH) DOMAIN, RESIDUES 409-556
Mutation: K465E
Gene Name(s): PDPK1 Gene View PDK1 Gene View

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.215
  • R-Value Work: 0.173
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 34.01 α = 90.00
b = 67.06 β = 90.00
c = 67.80 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-12-19
  • Released Date: 2008-05-13
  • Deposition author(s): Komander, D., Bayascas, J.R., Deak, M., Alessi, D.R., Van Aalten, D.M.F.

Revision History

  • 2011-07-13
    Type: Refinement description | Details: Fixed TLS group
  • 2011-07-13
    Type: Version format compliance | Details: Compliance with PDBx exchange dictionary V4
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor