MolNFT v1 · #84427 · protein
Structure of LC8 in complex with NEK9 phosphopeptide
3ZKF · Dynein light chain 1, cytoplasmic: “Structure of LC8 in complex with NEK9 phosphopeptide”. X-ray diffraction, 2 pockets (best druggability 0.77). MolNFT v1 #84427 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3ZKF
- Type
- protein
- Length
- 572 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dynein light chain 1, cytoplasmic; NEK9 protein
- UniProt
- P63167, Q6PKF2
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G, I, K | Dynein light chain 1, cytoplasmic | protein | 85 | 39% helix, 42% strand | P63167 |
| B, D, F, H, J, L | NEK9 protein | protein | 10 | 0% helix, 70% strand | Q6PKF2 |
| E | Dynein light chain 1, cytoplasmic | protein | 87 | 38% helix, 40% strand | P63167 |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 967 | 0.77 | 0.80 | 99 | empty |
| 2 | 115 | 0.48 | 0.80 | 18 | empty |
Interfaces
28 interfaces between chains.
- A–C · 954 Ų buried · 31 hydrogen bonds · protein-protein
- G–I · 952 Ų buried · 29 hydrogen bonds · protein-protein
- E–K · 948 Ų buried · 34 hydrogen bonds · protein-protein
- G–H · 680 Ų buried · 19 hydrogen bonds · protein-protein
- K–L · 672 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (phosphorylation).
Compared structures
- 3ZKF · Structure of LC8 in complex with Nek9 phosphopeptide · the same entry in another collection · chain L against L, 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 P63167
- Every structure of UniProt Q6PKF2
- Elsewhere: RCSB PDB 3ZKF · PDBe 3ZKF · UniProt P63167 · UniProt Q6PKF2
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