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Crystal structure of mouse PLK1-pbd in complex with phosphopeptide from HEF1 (799-809)

Analyse Crystal structure of mouse PLK1-pbd in complex with phosphopeptide from HEF1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5X3S
Type: protein
Length: 462 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SERINE/THREONINE-protein kinase PLK1; Peptide from enhancer of filamentation 1
EC: 2.7.11.21
UniProt: Q07832, Q14511
Pockets: 3 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A	SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21)	protein	223	30% helix, 27% strand	Q07832
C, D	Peptide from enhancer of filamentation 1	protein	8	0% helix, 38% strand	Q14511

Pockets

3 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	618	0.74	0.81	79	empty
2	99	0.36	0.74	22	empty
3	73	0.36	0.77	16	empty

Interfaces

5 interfaces between chains.

B–D · 576 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 555 Å² buried · 10 hydrogen bonds · protein-protein
B–A · 236 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 118 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 51 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 2 modified (phosphorylation).

Compared structures

5X3S · Crystal structure of mouse Plk1-PBD in complex with phosphopeptide from HEF1 (799-809) · the same entry in another collection · chain B against B, TM-score 1.00
Q07832 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase PLK1 (Q07832) · a predicted model of the same protein · chain B against A, TM-score 0.93
Q14511 · AlphaFold monomer V2.0 prediction for enhancer of filamentation 1 (Q14511) · a predicted model of the same protein · chain C against A, TM-score 0.45

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 Q07832
Every structure of UniProt Q14511
Elsewhere: RCSB PDB 5X3S · PDBe 5X3S · UniProt Q07832 · UniProt Q14511

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