MolNFT v1 · #76974 · protein
Crystal structure of selenomethionine incorporated apo D-serine deaminase from salmonella tyhimurium
3R0X · D-serine dehydratase: “Crystal structure of selenomethionine incorporated apo D-serine deaminase from salmonella tyhimurium”. X-ray diffraction, 2 ligands (NA, SO4), 1 pocket (best druggability 0.73). MolNFT v1 #76974 on GenesisL1…
- PDB
- 3R0X
- Type
- protein
- Length
- 438 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-serine dehydratase
- EC
- 4.3.1.18
- UniProt
- Q8ZL08
- Ligands
- NA, SO4
- Pockets
- 1 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 54% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-serine dehydratase (EC 4.3.1.18) | protein | 438 | 54% helix, 14% strand | Q8ZL08 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.73 | 0.98 | 24 | SO4, EDO |
Modifications
Observed in the structure: 13 modified (engineered).
Compared structures
- 3R0X · Crystal structure of Selenomethionine incorporated apo D-serine deaminase from Salmonella… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8ZL08 · AlphaFold monomer V2.0 prediction for D-serine dehydratase (Q8ZL08) · 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 Q8ZL08
- Elsewhere: RCSB PDB 3R0X · PDBe 3R0X · UniProt Q8ZL08
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