MolNFT v1 · #117599 · protein
Structure of the shigella flexneri vapc mutant D7N
5ED0 · TRNA(FMET)-specific endonuclease vapc: “Structure of the shigella flexneri vapc mutant D7N”. X-ray diffraction, 11 pockets (best druggability 0.76). MolNFT v1 #117599 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ED0
- Type
- protein
- Length
- 1,584 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA(FMET)-specific endonuclease vapc
- EC
- 3.1.-.-
- UniProt
- O06662
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | TRNA(FMET)-specific endonuclease vapc (EC 3.1.-.-) | protein | 132 | 57% helix, 12% strand | O06662 |
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 655 | 0.76 | 0.82 | 82 | empty |
| 2 | 452 | 0.68 | 0.80 | 43 | empty |
| 3 | 248 | 0.60 | 0.80 | 34 | empty |
| 4 | 138 | 0.41 | 0.74 | 23 | empty |
| 5 | 129 | 0.39 | 0.74 | 24 | empty |
Interfaces
22 interfaces between chains.
- A–I · 1147 Ų buried · 6 hydrogen bonds · protein-protein
- B–L · 1141 Ų buried · 6 hydrogen bonds · protein-protein
- C–K · 1098 Ų buried · 4 hydrogen bonds · protein-protein
- B–H · 481 Ų buried · 6 hydrogen bonds · protein-protein
- D–K · 320 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5ED0 · Structure of the Shigella flexneri VapC mutant D7N · the same entry in another collection · chain L against L, 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 O06662
- Elsewhere: RCSB PDB 5ED0 · PDBe 5ED0 · UniProt O06662
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