MolNFT v1 · #103398 · protein
Shewanella benthica dhdps with lysine and pyruvate
4PFM · 4-hydroxy-tetrahydrodipicolinate synthase: “Shewanella benthica dhdps with lysine and pyruvate”. X-ray diffraction, 2 ligands (LYS, NA), 4 pockets (best druggability 0.75). MolNFT v1 #103398 on GenesisL1: 3D structure, binding sites…
- PDB
- 4PFM
- 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
- A9DKW4
- Ligands
- LYS, NA
- Pockets
- 4 · best druggability 0.75
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 | 295 | 47% helix, 13% strand | A9DKW4 |
Ligands and binding sites
- LYS · Lysine · ligand · 3 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- FLC · Citrate anion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.75 | 0.86 | 51 | LYS |
| 2 | 147 | 0.47 | 0.77 | 27 | empty |
| 3 | 113 | 0.45 | 0.78 | 19 | empty |
| 4 | 67 | 0.32 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1435 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 4PFM · Shewanella benthica dhdps with lysine and pyruvate · the same entry in another collection · chain B against B, 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 A9DKW4
- Elsewhere: RCSB PDB 4PFM · PDBe 4PFM · UniProt A9DKW4
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