MolNFT v1 · #116761 · protein
Mouse polo-box domain and peptide analog 702
5DNJ · SERINE/THREONINE-protein kinase PLK1: “Mouse polo-box domain and peptide analog 702”. X-ray diffraction, 2 ligands (707, NH2), 1 pocket (best druggability 0.31). MolNFT v1 #116761 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5DNJ
- Type
- protein
- Length
- 218 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase PLK1; Peptide 707-56A-ser-tpo-NH2
- EC
- 2.7.11.21
- UniProt
- Q07832
- Ligands
- 707, NH2
- Pockets
- 1 · best druggability 0.31
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase PLK1 (EC 2.7.11.21) | protein | 215 | 30% helix, 30% strand | Q07832 |
| B | Peptide 707-56A-ser-tpo-NH2 | protein | 3 | 0% helix, 0% strand | — |
Ligands and binding sites
- 707 · N-(3-bromo-4-methoxybenzoyl)-beta-alanine · ligand · chains A, B
- NH2 · Amino group · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.31 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 519 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified, 1 covalent (covalent ligand, nonstandard, phosphorylation).
Compared structures
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
- Elsewhere: RCSB PDB 5DNJ · PDBe 5DNJ · UniProt Q07832
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