MolNFT v1 · #66789 · protein
Structure of the type III EFFECTOR/PHOSPHOTHREONINE lyase ospf from shigella flexneri
3I0U: “Structure of the type III EFFECTOR/PHOSPHOTHREONINE lyase ospf from shigella flexneri”. X-ray diffraction, 4 pockets (best druggability 0.51). MolNFT v1 #66789 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3I0U
- Type
- protein
- Length
- 393 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphothreonine lyase ospf
- EC
- 4.2.3.-
- UniProt
- Q8VSP9
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphothreonine lyase ospf (EC 4.2.3.-) | protein | 195 | 31% helix, 21% strand | Q8VSP9 |
| B | Phosphothreonine lyase ospf (EC 4.2.3.-) | protein | 198 | 34% helix, 20% strand | Q8VSP9 |
Ligands and binding sites
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 237 | 0.51 | 0.75 | 36 | empty |
| 2 | 53 | 0.40 | 0.81 | 10 | empty |
| 3 | 102 | 0.39 | 0.75 | 16 | empty |
| 4 | 115 | 0.35 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 491 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3I0U · Structure of the type III effector/phosphothreonine lyase OspF from Shigella flexneri · the same entry in another collection · chain A against A, TM-score 1.00
- Q8VSP9 · AlphaFold monomer V2.0 prediction for phosphothreonine lyase ospf (Q8VSP9) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q8VSP9
- Elsewhere: RCSB PDB 3I0U · PDBe 3I0U · UniProt Q8VSP9
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