4AW1

Human PDK1 Kinase Domain in Complex with Allosteric Compound PS210 Bound to the PIF-Pocket

Structural Biology Knowledgebase: 4AW1 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.186
  • R-Value Work: 0.164

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4AW1

Classification: TRANSFERASE

Total Structure Weight: 36643.94

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
Details: PHOSPHORYLATION AT S241
Gene Name(s): PDPK1 Gene View PDK1 Gene View

Small Molecules
Ligands 6 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)
21O
Query on 21O

A {(1R)-3-oxo-1-phenyl-3-[4-(trifluoromethyl)phenyl]propyl}propanedioic acid
C19 H15 F3 O5
MLJPLHGJBUWCBA-AWEZNQCLSA-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)
MN
Query on MN

A MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

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

A SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
SEP
Query on SEP
A L-PEPTIDE LINKING C3 H8 N O6 P SER

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 0.186
  • R-Value Work: 0.164
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 145.65 α = 90.00
b = 42.67 β = 98.52
c = 46.33 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: Sequence database correspondence | Details: SEQADV, DBREF
  • 2012-10-10
    Type: Polymer description | Details: COMPND
  • 2012-10-10
    Type: Secondary structure | Details: SHEET, HELIX
  • 2012-10-10
    Type: Other | Details: REMARK 700, REMARK 650, MASTER