MolNFT v1 · #146856 · protein
Structure of salmonella effector SSEK3 E258Q mutant
6DUS · Type III secretion system effector protein: “Structure of salmonella effector SSEK3 E258Q mutant”. X-ray diffraction, 3 ligands (UDP, NAG, MG), 4 pockets (best druggability 0.77). MolNFT v1 #146856 on GenesisL1: 3D structure…
- PDB
- 6DUS
- Type
- protein
- Length
- 615 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type III secretion system effector protein
- UniProt
- A0A0H3NMP8
- Ligands
- UDP, NAG, MG
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type III secretion system effector protein | protein | 310 | 40% helix, 20% strand | A0A0H3NMP8 |
| B | Type III secretion system effector protein | protein | 305 | 41% helix, 22% strand | A0A0H3NMP8 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 485 | 0.77 | 0.85 | 55 | UDP, NAG, MG, TRS |
| 2 | 574 | 0.77 | 0.83 | 62 | empty |
| 3 | 281 | 0.67 | 0.82 | 42 | UDP, NAG, MG |
| 4 | 59 | 0.32 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 830 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6DUS · Structure of Salmonella Effector SseK3 E258Q mutant · 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 A0A0H3NMP8
- Elsewhere: RCSB PDB 6DUS · PDBe 6DUS · UniProt A0A0H3NMP8
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