Research workbench
Dihydrodipicolinate synthase mutant S48F with lysine in the allosteric site and pyruvate in the catalytic site
Analyse Dihydrodipicolinate synthase mutant S48F with lysine in the allosteric site and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JZG
- Type
- protein
- Length
- 584 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxy-tetrahydrodipicolinate synthase
- EC
- 4.3.3.7
- UniProt
- A0A066Q637
- Ligands
- LYS, K
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 292 | 47% helix, 13% strand | A0A066Q637 |
Ligands and binding sites
- LYS · Lysine · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 3 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains B, 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 | 256 | 0.63 | 0.81 | 36 | LYS |
| 2 | 93 | 0.48 | 0.81 | 20 | empty |
| 3 | 101 | 0.44 | 0.79 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1300 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 7JZG · Dihydrodipicolinate synthase mutant S48F with lysine in the allosteric site and pyruvate… · 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 A0A066Q637
- Elsewhere: RCSB PDB 7JZG · PDBe 7JZG · UniProt A0A066Q637
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