MolNFT v1 · #159907 · protein
1.65 ångström ternary complex of deoxyhypusine synthase with cofactor NAD and spermidine mimic inhibitor GC7
6P4V: “1.65 ångström ternary complex of deoxyhypusine synthase with cofactor NAD and spermidine mimic inhibitor GC7”. X-ray diffraction, 2 ligands (NAD, GC7), 8 pockets (best druggability 0.86). MolNFT v1 #159907 on GenesisL1: 3D…
- PDB
- 6P4V
- Type
- protein
- Length
- 660 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyhypusine synthase
- EC
- 2.5.1.46
- UniProt
- P49366
- Ligands
- NAD, GC7
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyhypusine synthase (EC 2.5.1.46) | protein | 336 | 53% helix, 12% strand | P49366 |
| B | Deoxyhypusine synthase (EC 2.5.1.46) | protein | 324 | 52% helix, 13% strand | P49366 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- GC7 · 1-guanidinium-7-aminoheptane · ligand · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 949 | 0.86 | 0.87 | 111 | NAD, GC7 |
| 2 | 51 | 0.61 | 0.94 | 16 | empty |
| 3 | 173 | 0.47 | 0.76 | 23 | empty |
| 4 | 126 | 0.42 | 0.76 | 18 | empty |
| 5 | 81 | 0.41 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 3000 Ų buried · 50 hydrogen bonds · protein-protein
Compared structures
- 6P4V · 1.65 Angstrom ternary complex of Deoxyhypusine synthase with cofactor NAD and spermidine… · the same entry in another collection · chain A against A, TM-score 1.00
- P49366 · AlphaFold monomer V2.0 prediction for deoxyhypusine synthase (P49366) · a predicted model of the same protein · chain B 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 P49366
- Elsewhere: RCSB PDB 6P4V · PDBe 6P4V · UniProt P49366
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.