MolNFT v1 · #105694 · protein
Crystal structure of PLK1 polo-box domain in complex with pl-2
4RCP · SERINE/THREONINE-protein kinase PLK1: “Crystal structure of PLK1 polo-box domain in complex with pl-2”. X-ray diffraction, 2 ligands (ACE, NH2), 2 pockets (best druggability 0.42). MolNFT v1 #105694 on GenesisL1: 3D structure…
- PDB
- 4RCP
- Type
- protein
- Length
- 226 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase PLK1; Pl-2
- EC
- 2.7.11.21
- UniProt
- P53350
- Ligands
- ACE, NH2
- Pockets
- 2 · best druggability 0.42
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21) | protein | 223 | 31% helix, 29% strand | P53350 |
| B | Pl-2 | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A, B
- NH2 · Amino group · ion · chains A, B
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.42 | 0.82 | 22 | empty |
| 2 | 86 | 0.35 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 529 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified, 1 covalent (covalent ligand, nonstandard, phosphorylation).
Compared structures
- 4RCP · Crystal structure of Plk1 Polo-box domain in complex with PL-2 · 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 P53350
- Elsewhere: RCSB PDB 4RCP · PDBe 4RCP · UniProt P53350
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