MolNFT v1 · #123489 · protein
Crystal structure of mycobacterium avium SERB2 with serine present at slightly different position near act domain
5JLR · Phosphoserine phosphatase: “Crystal structure of mycobacterium avium SERB2 with serine present at slightly different position near act…”. X-ray diffraction, 2 ligands (SER, MG), 3 pockets (best druggability 0.73). MolNFT v1 #123489…
- PDB
- 5JLR
- Type
- protein
- Length
- 396 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoserine phosphatase
- EC
- 3.1.3.3
- UniProt
- A0QJI1
- Ligands
- SER, MG
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoserine phosphatase (EC 3.1.3.3) | protein | 396 | 41% helix, 28% strand | A0QJI1 |
Ligands and binding sites
- SER · Serine · ligand · chains A
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · chains A
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.73 | 0.98 | 23 | MG, EDO |
| 2 | 73 | 0.41 | 0.79 | 17 | empty |
| 3 | 55 | 0.32 | 0.77 | 17 | empty |
Compared structures
- 5JLR · Crystal structure of Mycobacterium avium SerB2 with serine present at slightly different… · the same entry in another collection · chain A against A, TM-score 1.00
- A0QJI1 · AlphaFold monomer V2.0 prediction for phosphoserine phosphatase (A0QJI1) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 A0QJI1
- Elsewhere: RCSB PDB 5JLR · PDBe 5JLR · UniProt A0QJI1
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