Research workbench
Structure of tssk from T6SS eaec in complex with nanobody NB18
Analyse Structure of tssk from T6SS eaec in complex with nanobody NB18 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M30
- Type
- protein
- Length
- 1,335 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type VI secretion protein; Anti-vesicular stomatitis virus N vhh
- UniProt
- A0A0P7QEP7
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 28% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type VI secretion protein | protein | 284 | 37% helix, 21% strand | A0A0P7QEP7 |
| B | Type VI secretion protein | protein | 405 | 33% helix, 26% strand | A0A0P7QEP7 |
| C | Type VI secretion protein | protein | 282 | 39% helix, 21% strand | A0A0P7QEP7 |
| D | Anti-vesicular stomatitis virus N vhh | protein | 119 | 5% helix, 61% strand | — |
| E | Anti-vesicular stomatitis virus N vhh | protein | 123 | 5% helix, 59% strand | — |
| F | Anti-vesicular stomatitis virus N vhh | protein | 122 | 5% helix, 60% strand | — |
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 300 | 0.85 | 0.95 | 32 | empty |
| 2 | 180 | 0.83 | 0.98 | 28 | empty |
| 3 | 932 | 0.82 | 0.83 | 93 | empty |
| 4 | 396 | 0.72 | 0.83 | 52 | empty |
| 5 | 366 | 0.66 | 0.80 | 43 | empty |
Interfaces
8 interfaces between chains.
- A–B · 1631 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1516 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1447 Ų buried · 11 hydrogen bonds · protein-protein
- A–E · 796 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 771 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5M30 · Structure of TssK from T6SS EAEC in complex with nanobody nb18 · 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 A0A0P7QEP7
- Elsewhere: RCSB PDB 5M30 · PDBe 5M30 · UniProt A0A0P7QEP7
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