Research workbench
Human PLK1-pbd in complex with poloxime ((E)-4-(hydroxyimino)-2- isopropyl-5-methylcyclohexa-2,5-dienone)
Analyse Human PLK1-pbd in complex with poloxime ((E)-4-(hydroxyimino)-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4H71
- Type
- protein
- Length
- 438 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
- Ligands
- PXE
- Pockets
- 5 · best druggability 0.60
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 | 216 | 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
- PXE · 2-methyl-5-(1-methylethyl)cyclohexa-2,5-diene-1,4-dione 1-oxime · ligand · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 236 | 0.60 | 0.80 | 28 | empty |
| 2 | 146 | 0.44 | 0.76 | 23 | GOL, PXE |
| 3 | 136 | 0.42 | 0.75 | 23 | empty |
| 4 | 54 | 0.37 | 0.80 | 14 | empty |
| 5 | 57 | 0.30 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- B–A · 334 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4H71 · Human Plk1-PBD in complex with Poloxime ((E)-4-(hydroxyimino)-2-isopropyl-5-methylcyclohex… · 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 4H71 · PDBe 4H71 · UniProt P53350
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