Research workbench
1.65 ångström ternary complex of deoxyhypusine synthase with cofactor NAD and spermidine mimic inhibitor GC7
Analyse 1.65 ångström ternary complex of deoxyhypusine synthase with cofactor NAD and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
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