MolNFT v1 · #124920 · protein
Dihydrodipicolinate synthase from the industrial and evolutionarily important cyanobacteria anabaena variabilis.
5KTL · 4-hydroxy-tetrahydrodipicolinate synthase: “Dihydrodipicolinate synthase from the industrial and evolutionarily important cyanobacteria anabaena…”. X-ray diffraction, 1 ligand (MN), 3 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 5KTL
- Type
- protein
- Length
- 590 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
- Q3M723
- Ligands
- MN
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) | protein | 295 | 48% helix, 13% strand | Q3M723 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 7 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 466 | 0.72 | 0.82 | 63 | MN |
| 2 | 168 | 0.60 | 0.83 | 22 | empty |
| 3 | 178 | 0.60 | 0.82 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1286 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 5KTL · Dihydrodipicolinate synthase from the industrial and evolutionarily important… · 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 Q3M723
- Elsewhere: RCSB PDB 5KTL · PDBe 5KTL · UniProt Q3M723
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