Research workbench
Crystal structure of human deoxyhypusine synthase in complex with spermidine and NAD
Analyse Crystal structure of human deoxyhypusine synthase in complex with spermidine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XXJ
- Type
- protein
- Length
- 692 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
- SPD, NAD, OXM
- Pockets
- 7 · 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 | 356 | 51% helix, 12% strand | P49366 |
| B | Deoxyhypusine synthase (EC 2.5.1.46) | protein | 336 | 53% helix, 12% strand | P49366 |
Ligands and binding sites
- SPD · Spermidine · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- OXM · Oxamic acid · ligand · chains B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
- FMT · Formic acid · additive · 5 copies · chains A, B
- ACT · Acetate ion · additive · 4 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 4 copies · chains A, B
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains B
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 889 | 0.86 | 0.88 | 106 | SPD, NAD, BME, FMT |
| 2 | 58 | 0.65 | 0.94 | 14 | empty |
| 3 | 175 | 0.52 | 0.78 | 20 | empty |
| 4 | 203 | 0.50 | 0.76 | 24 | EDO |
| 5 | 127 | 0.39 | 0.74 | 30 | EDO |
Interfaces
1 interface between chains.
- A–B · 2990 Ų buried · 47 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 6XXJ · Crystal Structure of Human Deoxyhypusine Synthase in complex with spermidine and NAD · 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 0.99
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 6XXJ · PDBe 6XXJ · UniProt P49366
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