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Plk-1 polo-box domain in complex with bioactive imidazolium-containing phosphopeptide macrocycle 3C

Analyse Plk-1 polo-box domain in complex with bioactive imidazolium-containing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4X9V
Type: protein
Length: 222 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SERINE/THREONINE-protein kinase PLK1; Phosphopeptide macrocycle 3C
EC: 2.7.11.21
UniProt: P53350
Ligands: NH2
Pockets: 2 · best druggability 0.37

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21)	protein	217	30% helix, 30% strand	P53350
B	Phosphopeptide macrocycle 3C	protein	5	0% helix, 20% strand	—

Ligands and binding sites

NH2 · Amino group · ion · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	55	0.37	0.79	13	empty
2	112	0.37	0.74	20	empty

Interfaces

1 interface between chains.

A–B · 664 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 modified (nonstandard, phosphorylation).

Compared structures

4X9V · PLK-1 polo-box domain in complex with Bioactive Imidazolium-containing phosphopeptide… · the same entry in another collection · chain A against A, TM-score 1.00

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 P53350
Elsewhere: RCSB PDB 4X9V · PDBe 4X9V · UniProt P53350

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