Research workbench
Structure of the eaec T6SS component tssk N-terminal domain in complex with llama nanobodies NBK18 and NBK27
Analyse Structure of the eaec T6SS component tssk N-terminal domain in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MWN
- Type
- protein
- Length
- 1,415 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type VI secretion protein; Llama nanobody raised against tssk, NBK18; Llama nanobody…
- UniProt
- A0A0P7QEP7
- Ligands
- PO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 27% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type VI secretion protein | protein | 312 | 36% helix, 25% strand | A0A0P7QEP7 |
| B | Type VI secretion protein | protein | 315 | 35% helix, 24% strand | A0A0P7QEP7 |
| C | Type VI secretion protein | protein | 313 | 37% helix, 24% strand | A0A0P7QEP7 |
| D, E | Llama nanobody raised against tssk, NBK18 | protein | 119 | 5% helix, 61% strand | — |
| F | Llama nanobody raised against tssk, NBK18 | protein | 120 | 5% helix, 61% strand | — |
| N | Llama nanobody raised against tssk, NBK27 | protein | 117 | 0% helix, 60% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.83 | 0.96 | 30 | empty |
| 2 | 176 | 0.82 | 0.97 | 24 | empty |
| 3 | 670 | 0.81 | 0.85 | 67 | empty |
| 4 | 746 | 0.80 | 0.83 | 79 | empty |
| 5 | 682 | 0.79 | 0.84 | 63 | empty |
Interfaces
11 interfaces between chains.
- B–C · 3062 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 2937 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 2791 Ų buried · 31 hydrogen bonds · protein-protein
- C–F · 843 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 824 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5MWN · Structure of the EAEC T6SS component TssK N-terminal domain in complex with llama… · 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 5MWN · PDBe 5MWN · UniProt A0A0P7QEP7
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