Research workbench
Crystal structure of the substrate binding domain of E.COLI dnak in complex with pyrrhocoricin
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
- 4EZN
- 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
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chaperone protein dnak | protein | 211 | 37% helix, 28% strand | P0A6Y8 |
| B | Chaperone protein dnak | protein | 215 | 42% helix, 28% strand | P0A6Y8 |
| C | Pyrrhocoricin | protein | 6 | 0% helix, 17% strand | P37362 |
| D | Pyrrhocoricin | protein | 9 | 0% helix, 22% strand | P37362 |
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 | 744 | 0.77 | 0.81 | 65 | empty |
| 2 | 506 | 0.76 | 0.84 | 45 | empty |
| 3 | 74 | 0.50 | 0.84 | 18 | empty |
| 4 | 98 | 0.48 | 0.81 | 20 | empty |
| 5 | 60 | 0.32 | 0.76 | 12 | empty |
Interfaces
5 interfaces between chains.
- A–C · 555 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 514 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 456 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 130 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 24 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4EZN · Crystal structure of the substrate binding domain of E.coli DnaK in complex with… · the same entry in another collection · chain D against D, 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 0.68
- 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 4EZN · PDBe 4EZN · UniProt P0A6Y8 · UniProt P37362
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.