MolNFT v1 · #140570 · protein
Regulatory domain of hypt M206Q mutant from salmonella typhimurium
5YEZ · Cell density-dependent motility repressor: “Regulatory domain of hypt M206Q mutant from salmonella typhimurium”. X-ray diffraction, 6 pockets (best druggability 0.75). MolNFT v1 #140570 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5YEZ
- Type
- protein
- Length
- 742 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell density-dependent motility repressor
- UniProt
- A0A0J5DK07
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell density-dependent motility repressor | protein | 200 | 32% helix, 30% strand | A0A0J5DK07 |
| B | Cell density-dependent motility repressor | protein | 201 | 28% helix, 30% strand | A0A0J5DK07 |
| C | Cell density-dependent motility repressor | protein | 169 | 31% helix, 35% strand | A0A0J5DK07 |
| D | Cell density-dependent motility repressor | protein | 172 | 28% helix, 31% strand | A0A0J5DK07 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 898 | 0.75 | 0.79 | 126 | empty |
| 2 | 364 | 0.73 | 0.85 | 68 | empty |
| 3 | 77 | 0.47 | 0.82 | 25 | empty |
| 4 | 103 | 0.40 | 0.76 | 15 | empty |
| 5 | 65 | 0.35 | 0.77 | 18 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1409 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1173 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 767 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 252 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 103 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5YEZ · Regulatory domain of HypT M206Q mutant from Salmonella typhimurium · 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 5YEZ · PDBe 5YEZ · UniProt A0A0J5DK07
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