MolNFT v1 · #150493 · protein
Structure of the type IV pilus from enterohemorrhagic escherichia COLI (ehec)
6GV9 · Prepilin peptidase-dependent protein D: “Structure of the type IV pilus from enterohemorrhagic escherichia COLI (ehec)”. Electron microscopy, 20 pockets (best druggability 0.89). MolNFT v1 #150493 on GenesisL1: 3D structure, binding…
- PDB
- 6GV9
- Type
- protein
- Length
- 1,960 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prepilin peptidase-dependent protein D
- UniProt
- Q8X974
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 1 distinct chain · 39% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N | Prepilin peptidase-dependent protein D | protein | 140 | 39% helix, 4% strand | Q8X974 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1106 | 0.89 | 0.90 | 144 | empty |
| 2 | 590 | 0.86 | 0.90 | 97 | empty |
| 3 | 350 | 0.80 | 0.89 | 58 | empty |
| 4 | 810 | 0.79 | 0.82 | 79 | empty |
| 5 | 245 | 0.78 | 0.91 | 50 | empty |
Interfaces
50 interfaces between chains.
- I–M · 722 Ų buried · 5 hydrogen bonds · protein-protein
- J–N · 719 Ų buried · 6 hydrogen bonds · protein-protein
- F–J · 715 Ų buried · 5 hydrogen bonds · protein-protein
- E–I · 707 Ų buried · 5 hydrogen bonds · protein-protein
- G–K · 704 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide (disulfide).
Compared structures
- 6GV9 · Structure of the type IV pilus from enterohemorrhagic Escherichia coli (EHEC) · the same entry in another collection · chain D against D, 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 Q8X974
- Elsewhere: RCSB PDB 6GV9 · PDBe 6GV9 · UniProt Q8X974
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