MolNFT v1 · #134763 · protein
Structure of 4-hydroxy-tetrahydrodipicolinate reductase from vibrio vulnificus with 2,5 furan dicarboxylic and NADH with intact polyhistidine tag
5TEN: “Structure of 4-hydroxy-tetrahydrodipicolinate reductase from vibrio vulnificus with 2,5 furan dicarboxylic…”. X-ray diffraction, 3 ligands (NAD, 7FN, SO4), 20 pockets (best druggability 0.86). MolNFT v1 #134763 on GenesisL1: 3D…
- PDB
- 5TEN
- Type
- protein
- Length
- 2,150 residues
- Chains
- 8
- 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, SO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G | 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) | protein | 269 | 37% helix, 26% strand | Q8DEM0 |
| H | 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8) | protein | 267 | 38% helix, 26% strand | Q8DEM0 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- 7FN · 2,5 Furan Dicarboxylic Acid · ligand · 8 copies · chains B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 19 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.86 | 0.90 | 52 | empty |
| 2 | 663 | 0.86 | 0.91 | 49 | empty |
| 3 | 412 | 0.74 | 0.84 | 48 | NAD, 7FN |
| 4 | 307 | 0.74 | 0.86 | 35 | NAD, 7FN |
| 5 | 410 | 0.73 | 0.83 | 49 | NAD, 7FN |
Interfaces
12 interfaces between chains.
- B–D · 1704 Ų buried · 38 hydrogen bonds · protein-protein
- E–F · 1662 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 1658 Ų buried · 37 hydrogen bonds · protein-protein
- G–H · 1637 Ų buried · 44 hydrogen bonds · protein-protein
- A–D · 1304 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 5TEN · Structure of 4-Hydroxy-tetrahydrodipicolinate Reductase from Vibrio vulnificus with 2,5… · the same entry in another collection · chain H against H, TM-score 1.00
- Q8DEM0 · AlphaFold monomer V2.0 prediction for 4-hydroxy- tetrahydrodipicolinate reductase (Q8DEM0) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 5TEN · PDBe 5TEN · UniProt Q8DEM0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.