5UPK: Serine/threonine-protein kinase PAK 4

CDC42 binds PAK4 via an extended GTPase-effector interface - 3 peptide: PAK4cat, PAK4-N45, CDC42. Determined by X-ray diffraction at 2.4 Å resolution. Released 27 Dec 2017.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,070
Mol. weight: 66.56 kDa
Ligands: ANP, GNP, MG
Released: 27 Dec 2017

Explore 5UPK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5UPK contains 32 α-helices and 23 β-strands across 3 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: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	1
α-helix	12-14	3
β-strand	15-23	9	1
β-strand	24-25	2	2
β-strand	32-33	2	2
α-helix	39-41	3

Chain B: 20 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	301-311	11
α-helix	317-319	3
β-strand	321-329	9	3
β-strand	334-340	7	3
β-strand	346-353	8	3
α-helix	354-356	3
α-helix	360-362	3
α-helix	363-372	10
β-strand	378	1	4
β-strand	381-387	7	3
β-strand	390-396	7	3
β-strand	401-402	2	4
α-helix	403-409	7
α-helix	414-433	20
β-strand	436-437	2	5
α-helix	443-445	3
β-strand	446-448	3	4
β-strand	454-456	3	4
β-strand	463-464	2	5
β-strand	472	1	6
α-helix	479-481	3
α-helix	484-487	4
β-strand	492	1	6
α-helix	495-510	16
α-helix	520-529	10
α-helix	531-533	3
α-helix	538-540	3
α-helix	543-552	10
α-helix	557-559	3
α-helix	561-562	2
α-helix	563-567	5
α-helix	570-574	5
α-helix	578-584	7

Chain C: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	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	117-120	4
α-helix	123-132	10
α-helix	139-149	11
β-strand	154-156	3	1
α-helix	165-178	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein kinase PAK 4	A	protein	48	Homo sapiens	O96013 (AlphaFold model)
Serine/threonine-protein kinase PAK 4	B	protein	346	Homo sapiens	O96013 (AlphaFold model)
Cell division control protein 42 homolog	C	protein	185	Homo sapiens	P60953 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5UPK_1 Serine/threonine-protein kinase PAK 4 (chains A)
SGSMFGKRKKRVEISAPSNFEHRVHTGFDQHEQKFTGLPRQWQSLIEE

Sequence of entity 2 (B), FASTA

>5UPK_2 Serine/threonine-protein kinase PAK 4 (chains B)
MGSSHHHHHHSSGLVPRGSHMENLYFQGARARQENGMPEKPPGPRSPQREPQRVSHEQFR
AALQLVVDPGDPRSYLDNFIKIGEGSTGIVCIATVRSSGKLVAVKKMDLRKQQRRELLFN
EVVIMRDYQHENVVEMYNSYLVGDELWVVMEFLEGGALTDIVTHTRMNEEQIAAVCLAVL
QALSVLHAQGVIHRDIKSDSILLTHDGRVKLSDFGFCAQVSKEVPRRKSLVGTPYWMAPE
LISRLPYGPEVDIWSLGIMVIEMVDGEPPYFNEPPLKAMKMIRDNLPPRLKNLHKVSPSL
KGFLDRLLVRDPAQRATAAELLKHPFLAKAGPPASIVPLMRQNRTR

Sequence of entity 3 (C), FASTA

>5UPK_3 Cell division control protein 42 homolog (chains C)
MQTIKCVVVGDGAVGKTCLLISYTTNKFPSEYVPTVFDNYAVTVMIGGEPYTLGLFDTAG
LEDYDRLRPLSYPQTDVFLVCFSVVSPSSFENVKEKWVPEITHHCPKTPFLLVGTQIDLR
DDPSTIEKLAKNKQKPITPETAEKLARDLKAVKYVECSALTQRGLKNVFDEAILAALLEH
HHHHH

Ligands and cofactors

ID	Name	Formula	Copies
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	1
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	1
MG	Magnesium ion	Mg	1

Primary citation

CDC42 binds PAK4 via an extended GTPase-effector interface. Ha, B.H., Boggon, T.J. Proc Natl Acad Sci U S A (2018) 115:531-536. DOI 10.1073/pnas.1717437115 · PubMed

Other PDB entries of the same protein (UniProt O96013 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2J0I 1.6 Å, Crystal structure of the human P21-activated kinase 4
2Q0N 1.75 Å, Structure of human p21 activating kinase 4 (PAK4) in complex with a consensus peptide
5VEF 1.75 Å, PAK4 kinase domain in complex with fasudil
5ZJW 1.8 Å, Crystal Structure of PAK4 in complex with inhibitor CZg353
5XVA 1.85 Å, Crystal Structure of PAK4 in complex with inhibitor CZH216
4JDI 1.85 Å, Crystal structure of Serine/threonine-protein kinase PAK 4 in complex with Paktide S…
8AHG 1.89 Å, PAC-FragmentDEL: Photoactivated covalent capture of DNA encoded fragments for hit…
6WLY 1.9 Å, PAK4 kinase domain in complex with LIMK1 Thr508 substrate peptide
7S48 1.9 Å, PAK4cat in complex with Integrin beta5 760-770 peptide
4FIH 1.97 Å, Catalytic domain of human PAK4 with QKFTGLPRQW peptide
4FII 2.0 Å, Catalytic domain of human PAK4 with RPKPLVDP peptide
4JDH 2.0 Å, Crystal structure of Serine/threonine-protein kinase PAK 4 in complex with Paktide T…

Browse structure collections

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