MolNFT v1 · #117598 · protein
Structure of the shigella flexneri vapc mutant D98N crystal form 2
5ECY · TRNA(FMET)-specific endonuclease vapc: “Structure of the shigella flexneri vapc mutant D98N crystal form 2”. X-ray diffraction, 16 pockets (best druggability 0.74). MolNFT v1 #117598 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5ECY
- Type
- protein
- Length
- 1,056 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA(FMET)-specific endonuclease vapc
- EC
- 3.1.-.-
- UniProt
- O06662
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 58% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | TRNA(FMET)-specific endonuclease vapc (EC 3.1.-.-) | protein | 132 | 58% helix, 12% strand | O06662 |
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 715 | 0.74 | 0.80 | 87 | empty |
| 2 | 243 | 0.70 | 0.86 | 44 | empty |
| 3 | 220 | 0.70 | 0.86 | 32 | empty |
| 4 | 207 | 0.55 | 0.78 | 48 | empty |
| 5 | 167 | 0.53 | 0.79 | 33 | empty |
Interfaces
15 interfaces between chains.
- B–D · 1141 Ų buried · 6 hydrogen bonds · protein-protein
- F–H · 1137 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 1128 Ų buried · 5 hydrogen bonds · protein-protein
- C–G · 1120 Ų buried · 5 hydrogen bonds · protein-protein
- C–F · 486 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5ECY · Structure of the Shigella flexneri VapC mutant D98N crystal form 2 · the same entry in another collection · chain H against H, TM-score 1.00
- O06662 · AlphaFold monomer V2.0 prediction for TRNA(FMET)-specific endonuclease vapc (O06662) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 5ECY · PDBe 5ECY · UniProt O06662
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