2ODB: Human cdc42

The crystal structure of human cdc42 in complex with the CRIB domain of human p21-activated kinase 6 (PAK6). Determined by X-ray diffraction at 2.4 Å resolution. Released 30 Jan 2007.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,719
Mol. weight: 26.31 kDa
Ligands: GCP, MG
Released: 30 Jan 2007

Explore 2ODB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2ODB contains 13 α-helices and 10 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 11 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	16-25	10
β-strand	37-46	10	1
β-strand	49-58	10	1
α-helix	62-64	3
α-helix	68-71	4
β-strand	77-83	7	1
α-helix	87-92	6
α-helix	93-97	5
α-helix	98-104	7
β-strand	110-115	6	1
α-helix	117-119	3
α-helix	123-130	8
α-helix	136-138	3
α-helix	139-149	11
β-strand	154-156	3	1
α-helix	165-177	13

Chain B: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	1
α-helix	13-15	3
β-strand	16-24	9	1
β-strand	25-27	3	2
β-strand	32-34	3	2
α-helix	38-44	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Human Cell Division Cycle 42 (CDC42)	A	protein	192	Homo sapiens	P60953 (AlphaFold model)
Serine/threonine-protein kinase PAK 6	B	protein	35		Q9NQU5 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2ODB_1 Human Cell Division Cycle 42 (CDC42) (chains A)
SMQTIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTLGLFDTA
GQEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQIDL
RDDPSTIEKLAKNKQKPITPETAEKLARDLKAVKYVECSALTQKGLKNVFDEAILAALEP
PEPKKSRRCVLL

Sequence of entity 2 (B), FASTA

>2ODB_2 Serine/threonine-protein kinase PAK 6 (chains B)
EISAPQNFQHRVHTSFDPKEGKFVGLPPQWQNILD

Ligands and cofactors

ID	Name	Formula	Copies
GCP	Phosphomethylphosphonic acid guanylate ester	C11 H18 N5 O13 P3	1
MG	Magnesium ion	Mg	1

Water and common crystallization additives (SO4, CL) are not listed.

Primary citation

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. et al. To be published.

Other PDB entries of the same protein (UniProt P60953 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2NGR 1.9 Å, Transition state complex for GTP hydrolysis by CDC42: comparisons of the high resolution…
4JS0 1.9 Å, Complex of Cdc42 with the CRIB-PR domain of IRSp53
6SUP 2.0 Å, Crystal Structure of TcdB2-TccC3-Cdc42
3VHL 2.08 Å, Crystal structure of the DHR-2 domain of DOCK8 in complex with Cdc42 (T17N mutant)
1GRN 2.1 Å, Crystal structure of the CDC42/CDC42GAP/ALF3 complex.
1NF3 2.1 Å, Structure of Cdc42 in a complex with the GTPase-binding domain of the cell polarity…
2DFK 2.15 Å, Crystal structure of the CDC42-Collybistin II complex
2WM9 2.2 Å, Structure of the complex between DOCK9 and Cdc42.
2WMO 2.2 Å, Structure of the complex between DOCK9 and Cdc42.
1GZS 2.3 Å, Crystal structure of the complex between the gef domain of the salmonella typhimurium…
1KI1 2.3 Å, Guanine Nucleotide Exchange Region of Intersectin in Complex with Cdc42
3GCG 2.3 Å, crystal structure of MAP and CDC42 complex

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