MolNFT v1 · #179230 · protein
Dihydrodipicolinate synthase S48F mutant with lysine in the allosteric site, and pyruvate and succinic semi-aldehyde in the catalytic site
7JZA · 4-hydroxy-tetrahydrodipicolinate synthase: “Dihydrodipicolinate synthase S48F mutant with lysine in the allosteric site, and pyruvate and succinic…”. X-ray diffraction, 2 ligands (LYS, K), 3 pockets (best druggability 0.63). MolNFT…
- PDB
- 7JZA
- 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 · 3 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 | 253 | 0.63 | 0.81 | 36 | LYS |
| 2 | 83 | 0.38 | 0.77 | 14 | empty |
| 3 | 100 | 0.37 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1304 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 7JZA · Dihydrodipicolinate synthase S48F mutant 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 7JZA · PDBe 7JZA · UniProt A0A066Q637
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