MolNFT v1 · #145181 · protein
Structure of salmonella effector SSEK3
6CGI · Type III secretion system effector protein: “Structure of salmonella effector SSEK3”. X-ray diffraction, 1 ligand (UDP), 9 pockets (best druggability 0.82). MolNFT v1 #145181 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6CGI
- Type
- protein
- Length
- 1,214 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type III secretion system effector protein
- UniProt
- A0A0H3NMP8
- Ligands
- UDP
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type III secretion system effector protein | protein | 304 | 39% helix, 22% strand | A0A0H3NMP8 |
| B | Type III secretion system effector protein | protein | 302 | 41% helix, 22% strand | A0A0H3NMP8 |
| C, D | Type III secretion system effector protein | protein | 304 | 40% helix, 22% strand | A0A0H3NMP8 |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1105 | 0.82 | 0.84 | 92 | empty |
| 2 | 985 | 0.74 | 0.77 | 95 | UDP |
| 3 | 321 | 0.64 | 0.80 | 36 | UDP |
| 4 | 186 | 0.56 | 0.80 | 18 | empty |
| 5 | 164 | 0.50 | 0.78 | 26 | UDP |
Interfaces
5 interfaces between chains.
- A–C · 920 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 901 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 421 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 124 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 96 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6CGI · Structure of Salmonella Effector SseK3 · 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 6CGI · PDBe 6CGI · UniProt A0A0H3NMP8
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