MolNFT v1 · #93556 · protein

Human PLK1-pbd with a glycerol bound at the phophopeptide binding site

4H5X · SERINE/THREONINE-protein kinase PLK1: “Human PLK1-pbd with a glycerol bound at the phophopeptide binding site”. X-ray diffraction, 4 pockets (best druggability 0.54). MolNFT v1 #93556 on GenesisL1: 3D structure, binding sites and…

PDB: 4H5X
Type: protein
Length: 440 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SERINE/THREONINE-protein kinase PLK1
EC: 2.7.11.21
UniProt: P53350
Pockets: 4 · best druggability 0.54

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21)	protein	218	34% helix, 30% strand	P53350
A	SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21)	protein	222	30% helix, 29% strand	P53350

Ligands and binding sites

GOL · Glycerol · additive · chains A

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

Pockets

4 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	212	0.54	0.78	36	empty
2	151	0.45	0.76	26	GOL
3	130	0.42	0.75	20	empty
4	53	0.37	0.80	14	empty

Interfaces

1 interface between chains.

B–A · 341 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

4H5X · human Plk1-PBD with a glycerol bound at the phophopeptide binding site · the same entry in another collection · chain B against B, 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 4H5X · PDBe 4H5X · UniProt P53350

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