MolNFT v1 · #6215 · protein
Crystal structure of phosphoserine phosphatase from methanococcus jannaschii
1F5S · Phosphoserine phosphatase (psp): “Crystal structure of phosphoserine phosphatase from methanococcus jannaschii”. X-ray diffraction, 2 ligands (MG, PO4), 5 pockets (best druggability 0.47). MolNFT v1 #6215 on GenesisL1: 3D structure…
- PDB
- 1F5S
- Type
- protein
- Length
- 419 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoserine phosphatase (psp)
- EC
- 3.1.3.3
- UniProt
- Q58989
- Ligands
- MG, PO4
- Pockets
- 5 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoserine phosphatase (psp) (EC 3.1.3.3) | protein | 210 | 48% helix, 22% strand | Q58989 |
| B | Phosphoserine phosphatase (psp) (EC 3.1.3.3) | protein | 209 | 48% helix, 23% strand | Q58989 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.47 | 0.84 | 22 | PO4 |
| 2 | 57 | 0.38 | 0.80 | 17 | empty |
| 3 | 79 | 0.36 | 0.77 | 19 | PO4 |
| 4 | 89 | 0.35 | 0.74 | 18 | empty |
| 5 | 51 | 0.27 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 522 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 1F5S · Crystal structure of phosphoserine phosphatase from methanococcus jannaschii · the same entry in another collection · chain A against A, TM-score 1.00
- Q58989 · AlphaFold monomer V2.0 prediction for phosphoserine phosphatase (Q58989) · a predicted model of the same protein · chain B 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 Q58989
- Elsewhere: RCSB PDB 1F5S · PDBe 1F5S · UniProt Q58989
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