Research workbench
Crystal structure of the substrate binding domain of E.COLI dnak in complex with PYRRHOCORICIN_LYZI (residues 1 to 10)
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
- 4HYB
- Type
- protein
- Length
- 441 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperone protein dnak; Pyrrhocoricin
- UniProt
- P0A6Y8, P37362
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chaperone protein dnak | protein | 213 | 40% helix, 28% strand | P0A6Y8 |
| B | Chaperone protein dnak | protein | 214 | 40% helix, 28% strand | P0A6Y8 |
| C, D | Pyrrhocoricin | protein | 7 | 0% helix, 29% strand | P37362 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 808 | 0.81 | 0.84 | 74 | SO4 |
| 2 | 96 | 0.53 | 0.84 | 22 | empty |
| 3 | 77 | 0.50 | 0.84 | 17 | empty |
| 4 | 79 | 0.39 | 0.78 | 15 | empty |
| 5 | 87 | 0.37 | 0.76 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–C · 589 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 570 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 496 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 35 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 4HYB · Crystal structure of the substrate binding domain of E.coli DnaK in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P37362 · AlphaFold monomer V2.0 prediction for pyrrhocoricin (P37362) · a predicted model of the same protein · chain C against A, TM-score 0.48
- P0A6Y8 · AlphaFold monomer V2.0 prediction for chaperone protein dnak (P0A6Y8) · a predicted model of the same protein · chain A against A, TM-score 0.47
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
- Every structure of UniProt P37362
- Elsewhere: RCSB PDB 4HYB · PDBe 4HYB · UniProt P0A6Y8 · UniProt P37362
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