MolNFT v1 · #146529 · protein
Rets kinase region without cobalt
6DK8 · Rets (regulator of exopolysaccharide and type III secretion): “Rets kinase region without cobalt”. X-ray diffraction, 1 ligand (NI), 20 pockets (best druggability 0.72). MolNFT v1 #146529 on GenesisL1: 3D structure, binding sites…
- PDB
- 6DK8
- Type
- protein
- Length
- 1,791 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rets (regulator of exopolysaccharide and type III secretion)
- UniProt
- Q9HUV7
- Ligands
- NI
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 8 distinct chains · 49% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rets (regulator of exopolysaccharide and type III secretion) | protein | 224 | 48% helix, 19% strand | Q9HUV7 |
| B | Rets (regulator of exopolysaccharide and type III secretion) | protein | 224 | 49% helix, 17% strand | Q9HUV7 |
| C | Rets (regulator of exopolysaccharide and type III secretion) | protein | 226 | 47% helix, 19% strand | Q9HUV7 |
| D | Rets (regulator of exopolysaccharide and type III secretion) | protein | 225 | 48% helix, 19% strand | Q9HUV7 |
| E | Rets (regulator of exopolysaccharide and type III secretion) | protein | 224 | 51% helix, 20% strand | Q9HUV7 |
| F | Rets (regulator of exopolysaccharide and type III secretion) | protein | 223 | 49% helix, 18% strand | Q9HUV7 |
| G | Rets (regulator of exopolysaccharide and type III secretion) | protein | 222 | 50% helix, 19% strand | Q9HUV7 |
| H | Rets (regulator of exopolysaccharide and type III secretion) | protein | 223 | 47% helix, 19% strand | Q9HUV7 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 20 copies · chains A, B, H, C, D, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 441 | 0.72 | 0.82 | 68 | NI |
| 2 | 504 | 0.71 | 0.81 | 60 | empty |
| 3 | 414 | 0.66 | 0.79 | 40 | empty |
| 4 | 320 | 0.64 | 0.80 | 42 | empty |
| 5 | 143 | 0.61 | 0.85 | 27 | empty |
Interfaces
9 interfaces between chains.
- G–H · 1756 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1730 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1726 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1696 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 696 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6DK8 · RetS kinase region without cobalt · 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 Q9HUV7
- Elsewhere: RCSB PDB 6DK8 · PDBe 6DK8 · UniProt Q9HUV7
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