MolNFT v1 · #140564 · protein
Regulatory domain of hypt from salmonella typhimurium (bromide ion- bound)
5YER · Cell density-dependent motility repressor: “Regulatory domain of hypt from salmonella typhimurium (bromide ion- bound)”. X-ray diffraction, 2 ligands (BR, SO4), 5 pockets (best druggability 0.59). MolNFT v1 #140564 on GenesisL1: 3D…
- PDB
- 5YER
- Type
- protein
- Length
- 415 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell density-dependent motility repressor
- UniProt
- A0A0J5DK07
- Ligands
- BR, SO4
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell density-dependent motility repressor | protein | 206 | 32% helix, 30% strand | A0A0J5DK07 |
| B | Cell density-dependent motility repressor | protein | 209 | 31% helix, 32% strand | A0A0J5DK07 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 211 | 0.59 | 0.81 | 38 | empty |
| 2 | 333 | 0.56 | 0.75 | 42 | empty |
| 3 | 144 | 0.47 | 0.77 | 28 | empty |
| 4 | 107 | 0.40 | 0.76 | 23 | empty |
| 5 | 97 | 0.40 | 0.77 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1117 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5YER · Regulatory domain of HypT from Salmonella typhimurium (Bromide ion-bound) · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A0J5DK07
- Elsewhere: RCSB PDB 5YER · PDBe 5YER · UniProt A0A0J5DK07
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