Research workbench
Crystal structure of the substrate binding domain of E.COLI dnak in complex with a short apidaecin peptide
Analyse Crystal structure of the substrate binding domain of E.COLI dnak in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E81
- Type
- protein
- Length
- 448 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperone protein dnak; Apidaecin peptide fragment
- UniProt
- P0A6Y8
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chaperone protein dnak | protein | 214 | 42% helix, 28% strand | P0A6Y8 |
| B | Chaperone protein dnak | protein | 218 | 42% helix, 27% strand | P0A6Y8 |
| C, D | Apidaecin peptide fragment | protein | 8 | 0% helix, 25% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.84 | 0.85 | 113 | empty |
| 2 | 158 | 0.55 | 0.81 | 23 | empty |
| 3 | 131 | 0.54 | 0.82 | 21 | empty |
| 4 | 182 | 0.46 | 0.75 | 20 | empty |
| 5 | 64 | 0.31 | 0.74 | 10 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1612 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 616 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 590 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 163 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 56 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4E81 · Crystal structure of the substrate binding domain of E.coli DnaK in complex with a short… · 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 0.50
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 4E81 · PDBe 4E81 · UniProt P0A6Y8
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