2ODB | pdb_00002odb

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.232 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history. 

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.

Macromolecule Content 

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

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Human Cell Division Cycle 42 (CDC42)192Homo sapiensMutation(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 Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60953
Sequence Annotations
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Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PAK 635Homo sapiensMutation(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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NQU5
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GCP

Query on GCP


Download:Ideal Coordinates CCD File
G [auth A]PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
PHBDHXOBFUBCJD-KQYNXXCUSA-N
SO4

Query on SO4


Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
H [auth B]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL

Query on CL


Download:Ideal Coordinates CCD File
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG


Download:Ideal Coordinates CCD File
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), 0.235 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 162.366α = 90
b = 162.366β = 90
c = 45.968γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MAR345data collection
MOSFLMdata reduction
CCP4data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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