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Crystal structure of an activated (thr->asp) polo-like kinase 1 (PLK1) catalytic domain in complex with wortmannin.
Analyse Crystal structure of an activated (thr->asp) polo-like kinase 1 (PLK1)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D5X
- Type
- protein
- Length
- 279 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polo-like kinase 1
- EC
- 2.7.11.21
- UniProt
- Q4KMI8
- Ligands
- KWT
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polo-like kinase 1 (EC 2.7.11.21) | protein | 279 | 34% helix, 20% strand | Q4KMI8 |
Ligands and binding sites
- KWT · (1s,6br,9as,11r,11br)-9A,11B-dimethyl-1-[(methyloxy) methyl]-3,6,9-trioxo-1,6,6B,7,8,9,9A,10,11,11B-decahydro-3H-furo[4, 3,2-de]indeno[4,5-h][2]benzopyran-11-yl acetate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 404 | 0.71 | 0.82 | 39 | KWT |
| 2 | 272 | 0.56 | 0.77 | 28 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3D5X · Crystal structure of an activated (Thr->Asp) Polo-like kinase 1 (Plk1) catalytic domain… · the same entry in another collection · chain A against A, 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 Q4KMI8
- Elsewhere: RCSB PDB 3D5X · PDBe 3D5X · UniProt Q4KMI8
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