Research workbench
Sdia in complex with 3-oxo-C8-homoserine lactone
Analyse Sdia in complex with 3-oxo-C8-homoserine lactone in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Y17
- Type
- protein
- Length
- 718 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator of ftsqaz gene cluster
- UniProt
- Q8XBD0
- Ligands
- LAE
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulator of ftsqaz gene cluster | protein | 238 | 49% helix, 13% strand | Q8XBD0 |
| B | Transcriptional regulator of ftsqaz gene cluster | protein | 237 | 49% helix, 14% strand | Q8XBD0 |
| C | Transcriptional regulator of ftsqaz gene cluster | protein | 243 | 51% helix, 13% strand | Q8XBD0 |
Ligands and binding sites
- LAE · 3-oxo-octanoic acid (2-oxo-tetrahydro-furan-3-yl)-amide · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.80 | 0.82 | 69 | empty |
| 2 | 129 | 0.79 | 0.96 | 21 | LAE |
| 3 | 128 | 0.79 | 0.96 | 21 | LAE |
| 4 | 138 | 0.77 | 0.94 | 25 | LAE |
| 5 | 117 | 0.47 | 0.79 | 19 | empty |
Interfaces
2 interfaces between chains.
- A–C · 1985 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 494 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4Y17 · SdiA in complex with 3-oxo-C8-homoserine lactone · 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 Q8XBD0
- Elsewhere: RCSB PDB 4Y17 · PDBe 4Y17 · UniProt Q8XBD0
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