4AW0

Human PDK1 Kinase Domain in Complex with Allosteric Compound PS182 Bound to the PIF-Pocket

Structural Biology Knowledgebase: 4AW0 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.188
  • R-Value Work: 0.170

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4AW0

Classification: TRANSFERASE

Total Structure Weight: 36601.92

Macromolecule Entities
Molecule Chains Length Organism Details
3-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1 A 311 Homo sapiens EC#: 2.7.11.1 IUBMB
Fragment: CATALYTIC DOMAIN, RESIDUES 51-359
Mutation: Y288G, Q292A
Gene Name(s): PDPK1 Gene View PDK1 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ATP
Query on ATP

A ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MJF
Query on MJF

A [(1R)-3-(4-chlorophenyl)-3-oxo-1-phenylpropyl]propanedioic acid
C18 H15 Cl O5
XOOQYQRTMFAOAP-AWEZNQCLSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DTD
Query on DTD

A DITHIANE DIOL
C4 H8 O2 S2
YPGMOWHXEQDBBV-IMJSIDKUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DMS
Query on DMS

A DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
SEP
Query on SEP
A L-PEPTIDE LINKING C3 H8 N O6 P SER
CME
Query on CME
A L-PEPTIDE LINKING C5 H11 N O3 S2 CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.188
  • R-Value Work: 0.170
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 148.27 α = 90.00
b = 44.01 β = 101.57
c = 47.39 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-05-30
  • Released Date: 2012-10-03
  • Deposition author(s): Schulze, J.O., Busschots, K., Lopez-Garcia, L.A., Lammi, C., Stroba, A., Zeuzem, S., Piiper, A., Alzari, P.M., Neimanis, S., Arencibia, J.M., Engel, M., Biondi, R.M.

Revision History

  • 2012-10-10
    Type: Secondary structure | Details: SHEET, HELIX
  • 2012-10-10
    Type: Other | Details: REMARK 700, REMARK 650, MASTER
  • 2012-10-10
    Type: Sequence database correspondence | Details: SEQADV, DBREF
  • 2012-10-10
    Type: Polymer description | Details: COMPND