Research workbench

PKA-S6K1 chimera with compound 1 (NU1085) bound

Analyse PKA-S6K1 chimera with compound 1 (NU1085) bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4C35
Type: protein
Length: 359 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Camp-dependent protein kinase catalytic subunit alpha; Camp-dependent protein kinase…
EC: 2.7.11.11
UniProt: P00517, Q3SX13
Ligands: NU3
Pockets: 2 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Camp-dependent protein kinase catalytic subunit alpha (EC 2.7.11.11)	protein	341	38% helix, 15% strand	P00517
I	Camp-dependent protein kinase inhibitor alpha	protein	18	39% helix, 0% strand	Q3SX13

Ligands and binding sites

NU3 · 2-(4-hydroxyphenyl)-1H-benzimidazole-4-carboxamide · ligand · chains A
MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	393	0.76	0.86	47	NU3
2	106	0.47	0.79	16	MPD

Interfaces

1 interface between chains.

A–I · 850 Å² buried · 18 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (phosphorylation).

Compared structures

4C35 · PKA-S6K1 Chimera with compound 1 (NU1085) bound · the same entry in another collection · chain A against A, TM-score 1.00
Q3SX13 · AlphaFold monomer V2.0 prediction for camp-dependent protein kinase inhibitor alpha… · a predicted model of the same protein · chain I against A, TM-score 0.43

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P00517
Every structure of UniProt Q3SX13
Elsewhere: RCSB PDB 4C35 · PDBe 4C35 · UniProt P00517 · UniProt Q3SX13

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