MolNFT v1 · #134759 · protein
Structure of 4-hydroxy-tetrahydrodipicolinate reductase from vibrio vulnificus with 2,5 furan dicarboxylic and NADH
5TEJ: “Structure of 4-hydroxy-tetrahydrodipicolinate reductase from vibrio vulnificus with 2,5 furan dicarboxylic…”. X-ray diffraction, 3 ligands (NAD, 7FN, NA), 16 pockets (best druggability 0.86). MolNFT v1 #134759 on GenesisL1: 3D…
- PDB
- 5TEJ
- Type
- protein
- Length
- 1,075 residues
- Chains
- 4
- 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, 7FN, NA
- Pockets
- 16 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) | protein | 269 | 37% helix, 26% strand | Q8DEM0 |
| C | 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) | protein | 268 | 37% helix, 26% strand | Q8DEM0 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- 7FN · 2,5 Furan Dicarboxylic Acid · ligand · 3 copies · chains B, C, D
- NA · Sodium ion · metal · 4 copies · chains B, C, D
- PG4 · Tetraethylene glycol · additive · chains A, C
- PGE · Triethylene glycol · additive · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 713 | 0.86 | 0.90 | 55 | empty |
| 2 | 432 | 0.74 | 0.84 | 48 | NAD, 7FN |
| 3 | 399 | 0.74 | 0.84 | 47 | NAD, 7FN |
| 4 | 417 | 0.73 | 0.83 | 44 | NAD, 7FN |
| 5 | 94 | 0.66 | 0.91 | 18 | empty |
Interfaces
6 interfaces between chains.
- B–D · 1666 Ų buried · 41 hydrogen bonds · protein-protein
- A–C · 1654 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 1286 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1209 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 163 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5TEJ · Structure of 4-Hydroxy-tetrahydrodipicolinate Reductase from Vibrio vulnificus with 2,5… · the same entry in another collection · chain D against D, 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 0.96
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 5TEJ · PDBe 5TEJ · UniProt Q8DEM0
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