MolNFT v1 · #96012 · protein

Crystal structure of polo-like kinase 1

4J7B: “Crystal structure of polo-like kinase 1”. X-ray diffraction, 15 pockets (best druggability 0.75). MolNFT v1 #96012 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4J7B
Type: protein
Length: 1,089 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polo-like kinase; 205 kda microtubule-associated protein
EC: 2.7.11.21
UniProt: Q6DRK7, P23226
Pockets: 15 · best druggability 0.75

Structure

x-ray diffraction · 4 distinct chains · 33% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Polo-like kinase (EC 2.7.11.21)	protein	284	37% helix, 20% strand	Q6DRK7
B, E	Polo-like kinase (EC 2.7.11.21)	protein	213	32% helix, 31% strand	Q6DRK7
C, F	205 kda microtubule-associated protein	protein	49	18% helix, 8% strand	P23226
D	Polo-like kinase (EC 2.7.11.21)	protein	281	33% helix, 20% strand	Q6DRK7

Pockets

15 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	593	0.75	0.82	63	empty
2	640	0.74	0.81	85	empty
3	246	0.55	0.77	33	empty
4	184	0.46	0.75	44	empty
5	100	0.46	0.79	23	empty

Interfaces

8 interfaces between chains.

E–F · 1995 Å² buried · 37 hydrogen bonds · protein-protein
B–C · 1975 Å² buried · 30 hydrogen bonds · protein-protein
A–B · 1208 Å² buried · 10 hydrogen bonds · protein-protein
D–E · 1193 Å² buried · 10 hydrogen bonds · protein-protein
C–E · 621 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4J7B · Crystal structure of polo-like kinase 1 · the same entry in another collection · chain C against C, TM-score 1.00
P23226 · AlphaFold monomer V2.0 prediction for 205 kda microtubule-associated protein (P23226) · a predicted model of the same protein · chain C against A, TM-score 0.30

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 Q6DRK7
Every structure of UniProt P23226
Elsewhere: RCSB PDB 4J7B · PDBe 4J7B · UniProt Q6DRK7 · UniProt P23226

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