2ODB

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)

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
View more details

wwPDB Validation 3D Report Full Report

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
Modelled Residue Count: 212
Deposited Residue Count: 227
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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 Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60953
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NQU5
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GCP Query on GCP Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER C₁₁ H₁₈ N₅ O₁₃ P₃ PHBDHXOBFUBCJD-KQYNXXCUSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B]	E [auth A], F [auth A], H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-01-30

Deposition Author(s):

Structural Genomics Consortium (SGC)

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