MolNFT v1 · #4339 · protein
The substrate binding domain of dnak in complex with a substrate peptide, determined from type 1 selenomethionyl crystals
1DKX: “The substrate binding domain of dnak in complex with a substrate peptide, determined from type 1…”. X-ray diffraction, 3 pockets (best druggability 0.54). MolNFT v1 #4339 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1DKX
- Type
- protein
- Length
- 226 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Substrate binding domain of dnak; Substrate peptide (7 residues)
- UniProt
- P0A6Y8
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Substrate binding domain of dnak | protein | 219 | 42% helix, 27% strand | P0A6Y8 |
| B | Substrate peptide (7 residues) | protein | 7 | 0% helix, 29% strand | — |
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 | 112 | 0.54 | 0.83 | 20 | empty |
| 2 | 85 | 0.34 | 0.74 | 15 | empty |
| 3 | 58 | 0.28 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 602 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1DKX · The substrate binding domain of dnak in complex with a substrate peptide, determined from… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A6Y8 · AlphaFold monomer V2.0 prediction for chaperone protein dnak (P0A6Y8) · a predicted model of the same protein · chain A against A, TM-score 0.48
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 P0A6Y8
- Elsewhere: RCSB PDB 1DKX · PDBe 1DKX · UniProt P0A6Y8
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