4A07

HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH ALLOSTERIC ACTIVATOR PS171 BOUND TO THE PIF-POCKET

Structural Biology Knowledgebase: 4A07 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.200
  • R-Value Work: 0.159

Literature

Macromolecules
Sequence Display for 4A07

Classification: TRANSFERASE

Total Structure Weight: 36901.03

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 50-359
Mutation: Y288G, Q292A
Gene Name(s): PDPK1 Gene View PDK1 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 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 NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
AZ7
Query on AZ7

A (3S)-3-(4-CHLOROPHENYL)-4-(5,7-DICHLORO-1H- BENZIMIDAZOL-2-YL)BUTANOIC ACID
C17 H13 Cl3 N2 O2
WMLLAHSMFYNLLO-JTQLQIEISA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
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
CSS
Query on CSS
A L-PEPTIDE LINKING C3 H7 N O2 S2 CYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.200
  • R-Value Work: 0.159
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 148.21 α = 90.00
b = 44.03 β = 101.23
c = 47.67 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-09-08
  • Released Date: 2011-12-07
  • Deposition author(s): Schulze, J.O., Lopez-Garcia, L.A., Froehner, W., Zhang, H., Navratil, J., Hindie, V., Zeuzem, S., Alzari, P.M., Neimanis, S., Engel, M., Biondi, R.M.

Revision History

  • 2011-12-21
    Type: Other | Details: Atom nomenclature