Research workbench
Crystal structure of wild-type plk-1 kinase domain in complex with a selective darpin
Analyse Crystal structure of wild-type plk-1 kinase domain in complex with a selective… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2V5Q
- Type
- protein
- Length
- 829 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase PLK1; Design ankyrin repeat protein
- EC
- 2.7.11.21
- UniProt
- P53350
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21) | protein | 285 | 37% helix, 20% strand | P53350 |
| C | Design ankyrin repeat protein | protein | 130 | 54% helix, 0% strand | — |
| D | Design ankyrin repeat protein | protein | 129 | 54% helix, 0% strand | — |
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 220 | 0.81 | 0.94 | 41 | empty |
| 2 | 416 | 0.72 | 0.82 | 50 | empty |
| 3 | 382 | 0.70 | 0.82 | 45 | empty |
| 4 | 434 | 0.63 | 0.77 | 47 | empty |
| 5 | 92 | 0.47 | 0.81 | 23 | empty |
Interfaces
4 interfaces between chains.
- A–D · 904 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 889 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 727 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 502 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2V5Q · Crystal structure of wild-type plk-1 kinase domain in complex with a selective darpin · the same entry in another collection · chain A against A, TM-score 1.00
- P53350 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase PLK1 (P53350) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 2V5Q · PDBe 2V5Q · UniProt P53350
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