2ODB | pdb_00002odb

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

• PDB DOI: https://doi.org/10.2210/pdb2ODB/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-12-22 Released: 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.205 (Depositor) 

Starting Model: experimental

Literature

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

Yang, X., Ugochukwu, E., Elkins, J., Soundararajan, M., Eswaran, J., Pike, A.C.W., Burgess, N., Debreczeni, J.E., Gileadi, O., Knapp, S., Doyle, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 4 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 26.31 kDa 
• Atom Count: 1,719 
• Modelled Residue Count: 212 
• Deposited Residue Count: 227 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Human Cell Division Cycle 42 (CDC42)	A	192	Homo sapiens	Mutation(s): 0  Gene Names: CDC42 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P60953 (Homo sapiens) Explore P60953  Go to UniProtKB:  P60953
PHAROS:  P60953 GTEx:  ENSG00000070831

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase PAK 6	B	35	Homo sapiens	Mutation(s): 0  Gene Names: PAK6 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NQU5 (Homo sapiens) Explore Q9NQU5  Go to UniProtKB:  Q9NQU5
PHAROS:  Q9NQU5 GTEx:  ENSG00000137843

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GCP	G [auth A]	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER C11 H18 N5 O13 P3 PHBDHXOBFUBCJD-KQYNXXCUSA-N
SO4	E [auth A], F [auth A], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.232 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.205 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.366	α = 90
b = 162.366	β = 90
c = 45.968	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• 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  

• Version 1.0: 2007-01-30
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description