Research workbench
The substrate binding domain of dnak in complex with a substrate peptide, determined from type 2 native crystals
Analyse The substrate binding domain of dnak in complex with a substrate peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DKY
- Type
- protein
- Length
- 422 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dnak; Peptide substrate
- UniProt
- P0A6Y8
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dnak | protein | 211 | 37% helix, 27% strand | P0A6Y8 |
| B | Dnak | protein | 203 | 37% helix, 27% strand | P0A6Y8 |
| C, D | Peptide substrate | protein | 4 | 0% helix, 50% strand | — |
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1058 | 0.76 | 0.78 | 64 | empty |
| 2 | 119 | 0.63 | 0.87 | 22 | empty |
| 3 | 108 | 0.55 | 0.84 | 23 | empty |
| 4 | 101 | 0.53 | 0.83 | 23 | empty |
| 5 | 112 | 0.38 | 0.74 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1137 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 392 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 386 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 54 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 49 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1DKY · 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 B against A, TM-score 0.49
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 1DKY · PDBe 1DKY · UniProt P0A6Y8
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