Research workbench
Structure of LC8 in complex with NEK9 peptide
Analyse Structure of LC8 in complex with NEK9 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZKE
- Type
- protein
- Length
- 575 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
- 4 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I, K | Dynein light chain 1, cytoplasmic | protein | 85 | 39% helix, 42% strand | P63167 |
| B, D, H, J, L | NEK9 protein | protein | 11 | 0% helix, 64% strand | Q6PKF2 |
| F | NEK9 protein | protein | 10 | 0% helix, 70% strand | Q6PKF2 |
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.70 | 0.96 | 18 | empty |
| 2 | 96 | 0.48 | 0.81 | 18 | empty |
| 3 | 78 | 0.29 | 0.72 | 17 | empty |
| 4 | 61 | 0.28 | 0.74 | 19 | empty |
Interfaces
21 interfaces between chains.
- I–K · 949 Ų buried · 32 hydrogen bonds · protein-protein
- E–G · 946 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 945 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 684 Ų buried · 18 hydrogen bonds · protein-protein
- I–J · 677 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3ZKE · Structure of LC8 in complex with Nek9 peptide · 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 3ZKE · PDBe 3ZKE · UniProt P63167 · UniProt Q6PKF2
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