MolNFT v1 · #91770 · protein
Structural characterization of thiaminase type II tena from staphylococcus aureus
4FN6 · Thiaminase-2: “Structural characterization of thiaminase type II tena from staphylococcus aureus”. X-ray diffraction, 10 pockets (best druggability 0.83). MolNFT v1 #91770 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4FN6
- Type
- protein
- Length
- 899 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thiaminase-2
- EC
- 3.5.99.2
- UniProt
- Q6GEY1
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Thiaminase-2 (EC 3.5.99.2) | protein | 225 | 75% helix, 0% strand | Q6GEY1 |
| C | Thiaminase-2 (EC 3.5.99.2) | protein | 224 | 73% helix, 0% strand | Q6GEY1 |
Ligands and binding sites
- ACT · Acetate ion · additive · 9 copies · chains A, B, C, D
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1012 | 0.83 | 0.84 | 102 | GOL, ACT |
| 2 | 390 | 0.78 | 0.87 | 37 | ACT |
| 3 | 280 | 0.76 | 0.88 | 38 | ACT |
| 4 | 386 | 0.76 | 0.85 | 38 | empty |
| 5 | 356 | 0.76 | 0.86 | 43 | GOL, ACT |
Interfaces
6 interfaces between chains.
- C–D · 1122 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1108 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 780 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 775 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 158 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (artifact).
Compared structures
- 4FN6 · Structural Characterization of Thiaminase type II TenA from Staphylococcus aureus · the same entry in another collection · chain A against A, TM-score 1.00
- Q6GEY1 · AlphaFold monomer V2.0 prediction for aminopyrimidine aminohydrolase (Q6GEY1) · 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 Q6GEY1
- Elsewhere: RCSB PDB 4FN6 · PDBe 4FN6 · UniProt Q6GEY1
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