9NBX: PAK1

Crystal structure of PAK1 bound to C2. Determined by X-ray diffraction at 2.15 Å resolution. Released 25 Jun 2025.

Method: X-ray diffraction
Resolution: 2.15 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,342
Mol. weight: 123.54 kDa
Ligands: A1BW5
Released: 25 Jun 2025

Explore 9NBX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9NBX contains 39 α-helices and 24 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: 19 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	252-260	9
β-strand	263	1	1
α-helix	266-268	3
β-strand	270-275	6	2
β-strand	285-289	5	2
β-strand	295-298	4	2
α-helix	310-320	11
β-strand	327	1	3
β-strand	330-332	3	2
β-strand	335	1	1
β-strand	343-345	3	2
β-strand	351	1	3
α-helix	352-358	7
α-helix	363-382	20
β-strand	385-386	2	4
α-helix	392-394	3
β-strand	395-397	3	3
β-strand	403-405	3	3
β-strand	412-413	2	4
β-strand	421	1	5
α-helix	428-430	3
α-helix	433-436	4
β-strand	441	1	5
α-helix	445-459	15
α-helix	469-479	11
α-helix	482-484	3
α-helix	487-489	3
α-helix	492-501	10
α-helix	510-511	2
α-helix	512-515	4
α-helix	519-523	5
α-helix	524-526	3
α-helix	527-530	4
α-helix	531-540	10

Chain B: 20 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	257-260	4
α-helix	262	1
α-helix	266-269	4
β-strand	270-275	6	6
β-strand	283-289	7	6
β-strand	295-302	8	6
α-helix	309-321	13
β-strand	327	1	7
α-helix	328-329	2
β-strand	330-336	7	6
β-strand	339-345	7	6
β-strand	351	1	7
α-helix	352-358	7
α-helix	363-382	20
α-helix	392-394	3
β-strand	395-397	3	7
β-strand	403-405	3	7
α-helix	423-424	2
α-helix	433-436	4
α-helix	444-459	16
α-helix	469-478	10
α-helix	487-489	3
α-helix	492-501	10
α-helix	510-511	2
α-helix	512-515	4
α-helix	519-523	5
α-helix	524-526	3
α-helix	527-530	4
α-helix	531-540	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutathione S-transferase class-mu 26 kDa isozyme,Serine/threonine-protein kinase PAK 1	A, B	protein	537	Homo sapiens	P08515 (AlphaFold model), Q13153 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9NBX_1 Glutathione S-transferase class-mu 26 kDa isozyme,Serine/threonine-protein kinase PAK 1 (chains A, B)
MHHHHHHHHGSPILGYWKIKGLVQPTRLLLEYLEEKYEEHLYERDEGDKWRNKKFELGLE
FPNLPYYIDGDVKLTQSMAIIRYIADKHNMLGGCPKERAEISMLEGAVLDIRYGVSRIAY
SKDFETLKVDFLSKLPEMLKMFKDRLCHKTYLNGDHVTHPDFMLYDALDVVLYMDPMCLD
AFPKLVCFKKRIEAIPQIDKYLKSSKYIAWPLQGWQATFGGGDHPPKSDGENLYFQGSDE
EILEKLRSIVSVGDPKKKYTRFEKIGQGASGTVYTAMDVATGQEVAIKQMNLQQQPKKEL
IINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCR
ECLQALEFLHSNQVIHRNIKSDNILLGMDGSVKLTDFGFCAQITPEQSKRSEMVGTPYWM
APEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPELQNPEKLS
AIFRDFLNRCLEMDVEKRGSAKELLQHQFLKIAKPLSSLTPLIAAAKEATKNNHGNS

Ligands and cofactors

ID	Name	Formula	Copies
A1BW5	(6M)-8-(3-aminopropyl)-6-(4-butoxy-2-methylphenyl)-2-(methylamino)pyrido[2,3-d]…	C22 H29 N5 O2	2

Water and common crystallization additives (DMS) are not listed.

Primary citation

Integrating Hydrogen Exchange with Molecular Dynamics for Improved Ligand Binding Predictions. Walters, B.T., Patapoff, A.W., Kiefer, J.R. et al. J Chem Inf Model (2025) 65:6144-6154. DOI 10.1021/acs.jcim.5c00397 · PubMed

Other PDB entries of the same protein (UniProt P08515 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8OK1 1.38 Å, WD repeat containing protein 5 (WDR5)- N225A mutant
6JI6 1.5 Å, Crystal structure of glutathione S-transferase complexed and modified with glutathione
6RWD 1.53 Å, Crystal structure of SjGST in complex with GSH and ellagic acid at 1.53 Angstrom…
4WR4 1.6 Å, Crystal Structure of GST Mutated with Halogenated Tyrosine (7bGST-1)
9NME 1.6 Å, SARS-CoV-2 3CLPro in complex with 2-[2-hydroxy-3-(4-isoquinolyl)-4-oxo-6-(trifluoromethyl…
8GYD 1.7 Å, Structure of Schistosoma japonicum Glutathione S-transferase bound with the ligand…
9N4U 1.77 Å, Crystal structure of PAK1 bound to compound R1
1DUG 1.8 Å, Structure of the fibrinogen G chain integrin binding and factor xiiia crosslinking sites…
9NMF 1.8 Å, SARS-CoV-2 3CLPro in complex with 8-(6-amino-3-pyridyl)-2-hydroxy-3-(4-isoquinolyl)-6-(tr…
7AL7 1.8 Å, The Crystal Structure of Human IL-18 in Complex With Human IL-18 Binding Protein
8OKF 1.85 Å, WD repeat containing protein 5 (WDR5)- PER2 peptide
9N48 1.85 Å, Crystal structure of PAK1 bound to compound C1

Browse structure collections

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