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Structure of a human PLK1 polo-box DOMAIN/PHOSPHOPEPTIDE complex

Analyse Structure of a human PLK1 polo-box DOMAIN/PHOSPHOPEPTIDE complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1UMW
Type: protein
Length: 458 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SERINE/THREONINE-protein kinase plk; Peptide
EC: 2.7.1.-
UniProt: P53350
Pockets: 2 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 28% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	SERINE/THREONINE-protein kinase plk (EC 2.7.1.-)	protein	222	29% helix, 30% strand	P53350
E, F	Peptide	protein	7	0% helix, 29% strand	—

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	707	0.70	0.77	69	empty
2	88	0.42	0.79	27	empty

Interfaces

4 interfaces between chains.

A–E · 551 Å² buried · 12 hydrogen bonds · protein-protein
B–F · 543 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 201 Å² buried · 1 hydrogen bond · protein-protein
B–E · 16 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (phosphorylation).

Compared structures

1UMW · Structure of a human Plk1 Polo-box domain/phosphopeptide complex · the same entry in another collection · chain A against A, TM-score 1.00
P53350 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase PLK1 (P53350) · a predicted model of the same protein · chain A against A, TM-score 0.94

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 1UMW · PDBe 1UMW · UniProt P53350

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