MolNFT v1 · #134762 · protein
Structure of 4-hydroxy-tetrahydrodipicolinate reductase from vibrio vulnificus with 2,6 pyridine dicarboxylic and NADH
5TEM: “Structure of 4-hydroxy-tetrahydrodipicolinate reductase from vibrio vulnificus with 2,6 pyridine dicarboxylic…”. X-ray diffraction, 3 ligands (NAD, PDC, SO4), 5 pockets (best druggability 0.72). MolNFT v1 #134762 on GenesisL1: 3D…
- PDB
- 5TEM
- Type
- protein
- Length
- 532 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 4-hydroxy-tetrahydrodipicolinate reductase
- EC
- 1.17.1.8
- UniProt
- Q8DEM0
- Ligands
- NAD, PDC, SO4
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A | 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) | protein | 266 | 38% helix, 24% strand | Q8DEM0 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains C, A
- PDC · Pyridine-2,6-dicarboxylic acid · ligand · 2 copies · chains C, A
- SO4 · Sulfate ion · ion · 4 copies · chains C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.72 | 0.84 | 46 | NAD, PDC |
| 2 | 365 | 0.71 | 0.83 | 46 | NAD, PDC |
| 3 | 396 | 0.56 | 0.74 | 41 | empty |
| 4 | 246 | 0.53 | 0.76 | 27 | empty |
| 5 | 225 | 0.52 | 0.76 | 29 | empty |
Interfaces
1 interface between chains.
- C–A · 241 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5TEM · Structure of 4-Hydroxy-tetrahydrodipicolinate Reductase from Vibrio vulnificus with 2,6… · the same entry in another collection · chain C against C, TM-score 1.00
- Q8DEM0 · AlphaFold monomer V2.0 prediction for 4-hydroxy- tetrahydrodipicolinate reductase (Q8DEM0) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q8DEM0
- Elsewhere: RCSB PDB 5TEM · PDBe 5TEM · UniProt Q8DEM0
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