Research workbench
Structure of cagy from a cryo-EM reconstruction of a T4SS
Analyse Structure of cagy from a cryo-EM reconstruction of a T4SS in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ODI
- Type
- protein
- Length
- 2,772 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type IV secretion system apparatus protein cagy
- UniProt
- A0A2J9KJK8
- Pockets
- 20 · best druggability 0.57
Structure
electron microscopy · 1 distinct chain · 14% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| b, c, d, e, f, g, h, i, j, k, l, m, n, o | Type IV secretion system apparatus protein cagy | protein | 198 | 14% helix, 27% strand | A0A2J9KJK8 |
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.57 | 0.77 | 50 | empty |
| 2 | 297 | 0.56 | 0.76 | 55 | empty |
| 3 | 253 | 0.54 | 0.76 | 35 | empty |
| 4 | 260 | 0.54 | 0.76 | 36 | empty |
| 5 | 239 | 0.54 | 0.77 | 31 | empty |
Interfaces
14 interfaces between chains.
- l–m · 1991 Ų buried · 16 hydrogen bonds · protein-protein
- n–o · 1910 Ų buried · 7 hydrogen bonds · protein-protein
- c–d · 1904 Ų buried · 8 hydrogen bonds · protein-protein
- b–o · 1899 Ų buried · 11 hydrogen bonds · protein-protein
- f–g · 1854 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6ODI · Structure of CagY from a cryo-EM reconstruction of a T4SS · 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 A0A2J9KJK8
- Elsewhere: RCSB PDB 6ODI · PDBe 6ODI · UniProt A0A2J9KJK8
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