Research workbench
T6SS protein tssm C-terminal domain (835-1129) from eaec
Analyse T6SS protein tssm C-terminal domain (835-1129) from eaec in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Y7M
- Type
- protein
- Length
- 725 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HI113 protein; Type VI secretion protein icmf
- UniProt
- A0A070IVV8
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | HI113 protein | protein | 129 | 9% helix, 50% strand | — |
| C | Type VI secretion protein icmf | protein | 241 | 30% helix, 31% strand | A0A070IVV8 |
| D | Type VI secretion protein icmf | protein | 226 | 29% helix, 31% strand | A0A070IVV8 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 398 | 0.65 | 0.79 | 69 | empty |
| 2 | 194 | 0.48 | 0.76 | 21 | empty |
| 3 | 157 | 0.46 | 0.76 | 26 | empty |
| 4 | 144 | 0.46 | 0.77 | 24 | empty |
| 5 | 155 | 0.45 | 0.76 | 23 | empty |
Interfaces
3 interfaces between chains.
- C–D · 843 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 591 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 568 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4Y7M · T6SS protein TssM C-terminal domain (835-1129) from EAEC · 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 A0A070IVV8
- Elsewhere: RCSB PDB 4Y7M · PDBe 4Y7M · UniProt A0A070IVV8
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