2ODB

The crystal structure of human cdc42 in complex with the CRIB domain of human p21-activated kinase 6 (PAK6)

Structural Biology Knowledgebase: 2ODB SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.232
  • R-Value Work: 0.203

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2ODB

Classification: PROTEIN BINDING

Total Structure Weight: 26306.52

Macromolecule Entities
Molecule Chains Length Organism Details
Human Cell Division Cycle 42 (CDC42) A 192 Homo sapiens Gene Name(s): CDC42 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Serine/threonine-protein kinase PAK 6 B 35 Homo sapiens EC#: 2.7.11.1 IUBMB
Fragment: PAK6 CRIB domain
Gene Name(s): PAK6 Gene View PAK5 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
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)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.232
  • R-Value Work: 0.203
  • Space Group: P 65 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 162.37 α = 90.00
b = 162.37 β = 90.00
c = 45.97 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-12-22
  • Released Date: 2007-01-30
  • Deposition author(s): Ugochukwu, E., Yang, X., Elkins, J., Soundararajan, M., Pike, A.C.W., Eswaran, J., Burgess, N., Debreczeni, J.E., Sundstrom, M., Arrowsmith, C., Weigelt, J., Edwards, A., Gileadi, O., von Delft, F., Knapp, S., Doyle, D., Structural Genomics Consortium (SGC)

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor