MolNFT v1 · #106150 · protein
Crystal structure of L-serine dehydratase from legionella pneumophila
4RQO: “Crystal structure of L-serine dehydratase from legionella pneumophila”. X-ray diffraction, 2 ligands (SF4, CL), 8 pockets (best druggability 0.75). MolNFT v1 #106150 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4RQO
- Type
- protein
- Length
- 892 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-serine dehydratase
- EC
- 4.3.1.17
- UniProt
- R9SE63
- Ligands
- SF4, CL
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-serine dehydratase (EC 4.3.1.17) | protein | 444 | 52% helix, 11% strand | R9SE63 |
| B | L-serine dehydratase (EC 4.3.1.17) | protein | 448 | 52% helix, 12% strand | R9SE63 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 400 | 0.75 | 0.85 | 58 | empty |
| 2 | 251 | 0.65 | 0.82 | 30 | empty |
| 3 | 272 | 0.64 | 0.81 | 24 | empty |
| 4 | 83 | 0.41 | 0.78 | 25 | empty |
| 5 | 98 | 0.37 | 0.74 | 15 | CL |
Interfaces
1 interface between chains.
- A–B · 2411 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 37 modified (engineered).
Compared structures
- 4RQO · Crystal structure of L-Serine Dehydratase from Legionella pneumophila · the same entry in another collection · 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 R9SE63
- Elsewhere: RCSB PDB 4RQO · PDBe 4RQO · UniProt R9SE63
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