Research workbench
T6SS protein tssm C-terminal domain (869-1107) from eaec
Analyse T6SS protein tssm C-terminal domain (869-1107) from eaec in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Y7O
- Type
- protein
- Length
- 725 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type VI secretion protein icmf; Type VI secretion system protein vasd
- UniProt
- A0A017IZH1, H4VA93
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 21% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Type VI secretion protein icmf | protein | 239 | 31% helix, 31% strand | A0A017IZH1 |
| C | Type VI secretion system protein vasd | protein | 123 | 10% helix, 48% strand | H4VA93 |
| D | Type VI secretion system protein vasd | protein | 124 | 14% helix, 45% strand | H4VA93 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 241 | 0.59 | 0.80 | 32 | empty |
| 2 | 193 | 0.52 | 0.78 | 20 | empty |
| 3 | 104 | 0.41 | 0.77 | 19 | empty |
| 4 | 108 | 0.40 | 0.76 | 14 | empty |
| 5 | 64 | 0.39 | 0.79 | 16 | empty |
Interfaces
4 interfaces between chains.
- A–B · 925 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 594 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 580 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 18 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4Y7O · T6SS protein TssM C-terminal domain (869-1107) from EAEC · the same entry in another collection · chain B against B, 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 A0A017IZH1
- Every structure of UniProt H4VA93
- Elsewhere: RCSB PDB 4Y7O · PDBe 4Y7O · UniProt A0A017IZH1 · UniProt H4VA93
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