MolNFT v1 · #90778 · protein
Crystal structure of yfkj from bacillus subtilis
4ETM · Low molecular weight protein-tyrosine-phosphatase yfkj: “Crystal structure of yfkj from bacillus subtilis”. X-ray diffraction, 3 ligands (NA, K, PO4), 4 pockets (best druggability 0.41). MolNFT v1 #90778 on GenesisL1: 3D structure…
- PDB
- 4ETM
- Type
- protein
- Length
- 321 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Low molecular weight protein-tyrosine-phosphatase yfkj
- EC
- 3.1.3.48
- UniProt
- O35016
- Ligands
- NA, K, PO4
- Pockets
- 4 · best druggability 0.41
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Low molecular weight protein-tyrosine-phosphatase yfkj (EC 3.1.3.48) | protein | 162 | 44% helix, 14% strand | O35016 |
| B | Low molecular weight protein-tyrosine-phosphatase yfkj (EC 3.1.3.48) | protein | 159 | 45% helix, 14% strand | O35016 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.41 | 0.80 | 15 | empty |
| 2 | 81 | 0.36 | 0.76 | 23 | empty |
| 3 | 58 | 0.32 | 0.76 | 16 | empty |
| 4 | 74 | 0.31 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 476 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4ETM · Crystal structure of YfkJ from Bacillus subtilis · the same entry in another collection · chain A against A, TM-score 1.00
- O35016 · AlphaFold monomer V2.0 prediction for low molecular weight protein- tyrosine-phosphatase… · a predicted model of the same protein · chain B 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 O35016
- Elsewhere: RCSB PDB 4ETM · PDBe 4ETM · UniProt O35016
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