Research workbench
Crystal structure of ASN173SER variant of human deoxyhypusine synthase in complex with NAD and spermidine
Analyse Crystal structure of ASN173SER variant of human deoxyhypusine synthase in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A6T
- Type
- protein
- Length
- 664 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, SPD, OXM
- 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 | 52% helix, 12% strand | P49366 |
| B | Deoxyhypusine synthase (EC 2.5.1.46) | protein | 328 | 52% helix, 13% strand | P49366 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- SPD · Spermidine · ligand · 2 copies · chains A, B
- OXM · Oxamic acid · ligand · chains B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 939 | 0.86 | 0.87 | 110 | NAD, SPD, EDO |
| 2 | 169 | 0.52 | 0.79 | 21 | EDO |
| 3 | 70 | 0.52 | 0.86 | 19 | empty |
| 4 | 127 | 0.42 | 0.76 | 28 | empty |
| 5 | 51 | 0.39 | 0.82 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2966 Ų buried · 49 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 modified (disulfide, oxidation).
Compared structures
- 7A6T · Crystal Structure of Asn173Ser variant of Human Deoxyhypusine Synthase in complex with… · 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 7A6T · PDBe 7A6T · UniProt P49366
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