MolNFT v1 · #64349 · protein
Dihydrodipicolinate synthase from salmonella typhimurium LT2
3G0S: “Dihydrodipicolinate synthase from salmonella typhimurium LT2”. X-ray diffraction, 2 ligands (MG, CL), 3 pockets (best druggability 0.74). MolNFT v1 #64349 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3G0S
- Type
- protein
- Length
- 589 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydrodipicolinate synthase
- EC
- 4.2.1.52
- UniProt
- Q8ZN71
- Ligands
- MG, CL
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 295 | 46% helix, 13% strand | Q8ZN71 |
| B | Dihydrodipicolinate synthase (EC 4.2.1.52) | protein | 294 | 48% helix, 13% strand | Q8ZN71 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
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 | 434 | 0.74 | 0.83 | 50 | GOL |
| 2 | 132 | 0.50 | 0.80 | 26 | empty |
| 3 | 131 | 0.47 | 0.78 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1332 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3G0S · Dihydrodipicolinate synthase from Salmonella typhimurium LT2 · the same entry in another collection · chain A against A, TM-score 1.00
- Q8ZN71 · AlphaFold monomer V2.0 prediction for 4-hydroxy- tetrahydrodipicolinate synthase (Q8ZN71) · 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 Q8ZN71
- Elsewhere: RCSB PDB 3G0S · PDBe 3G0S · UniProt Q8ZN71
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