Research workbench
Structure of the shigella flexneri vapc mutant D98N crystal form 1
Analyse Structure of the shigella flexneri vapc mutant D98N crystal form 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ECD
- Type
- protein
- Length
- 264 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA(FMET)-specific endonuclease vapc
- EC
- 3.1.-.-
- UniProt
- O06662
- Pockets
- 1 · best druggability 0.31
Structure
x-ray diffraction · 1 distinct chain · 58% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | TRNA(FMET)-specific endonuclease vapc (EC 3.1.-.-) | protein | 132 | 58% helix, 12% strand | O06662 |
Ligands and binding sites
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.31 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1111 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5ECD · Structure of the Shigella flexneri VapC mutant D98N crystal form 1 · the same entry in another collection · chain A against A, 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 5ECD · PDBe 5ECD · UniProt O06662
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