Research workbench
Crystal structure of DLC8 in complex with panoramix TQT+TQ peptide
Analyse Crystal structure of DLC8 in complex with panoramix TQT+TQ peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K3J
- Type
- protein
- Length
- 581 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dynein light chain 1, cytoplasmic; Protein panoramix
- UniProt
- Q24117, Q9W2H9
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G, I | Dynein light chain 1, cytoplasmic | protein | 85 | 38% helix, 46% strand | Q24117 |
| B | Protein panoramix | protein | 25 | 12% helix, 56% strand | Q9W2H9 |
| D, F | Protein panoramix | protein | 11 | 0% helix, 64% strand | Q9W2H9 |
| H | Protein panoramix | protein | 25 | 0% helix, 60% strand | Q9W2H9 |
| K | Dynein light chain 1, cytoplasmic | protein | 84 | 38% helix, 45% strand | Q24117 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, C, G, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.64 | 0.76 | 55 | empty |
| 2 | 214 | 0.47 | 0.74 | 29 | SO4 |
| 3 | 68 | 0.39 | 0.79 | 21 | empty |
Interfaces
17 interfaces between chains.
- A–G · 934 Ų buried · 24 hydrogen bonds · protein-protein
- I–K · 837 Ų buried · 25 hydrogen bonds · protein-protein
- G–H · 811 Ų buried · 20 hydrogen bonds · protein-protein
- B–I · 759 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 579 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 7K3J · Crystal structure of dLC8 in complex with Panoramix TQT+TQ peptide · the same entry in another collection · chain K against K, TM-score 1.00
- Q24117 · AlphaFold monomer V2.0 prediction for dynein light chain 1, cytoplasmic (Q24117) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q24117
- Every structure of UniProt Q9W2H9
- Elsewhere: RCSB PDB 7K3J · PDBe 7K3J · UniProt Q24117 · UniProt Q9W2H9
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