MolNFT v1 · #116738 · protein

Mouse polo-box domain and EMI2 (169-177)

5DMS · SERINE/THREONINE-protein kinase PLK1: “Mouse polo-box domain and EMI2 (169-177)”. X-ray diffraction, 2 pockets (best druggability 0.65). MolNFT v1 #116738 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5DMS
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; F-box only protein 43
EC: 2.7.11.21
UniProt: Q07832, Q8CDI2
Pockets: 2 · best druggability 0.65

Structure

x-ray diffraction · 4 distinct chains · 30% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21)	protein	226	31% helix, 29% strand	Q07832
B	F-box only protein 43	protein	5	0% helix, 20% strand	Q8CDI2
C	SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21)	protein	222	28% helix, 29% strand	Q07832
D	F-box only protein 43	protein	9	33% helix, 11% strand	Q8CDI2

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	456	0.65	0.77	40	empty
2	288	0.52	0.75	32	empty

Interfaces

4 interfaces between chains.

C–D · 617 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 452 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 403 Å² buried · 1 hydrogen bond · protein-protein
A–D · 12 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (phosphorylation).

Compared structures

5DMS · Mouse Polo-box domain and Emi2 (169-177) · the same entry in another collection · chain D against D, 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 A against A, TM-score 0.93
Q8CDI2 · AlphaFold monomer V2.0 prediction for F-box only protein 43 (Q8CDI2) · a predicted model of the same protein · chain D against A, TM-score 0.56

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 Q8CDI2
Elsewhere: RCSB PDB 5DMS · PDBe 5DMS · UniProt Q07832 · UniProt Q8CDI2

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