MolNFT v1 · #172576 · protein
Crystal structure of ASN173SER variant of human deoxyhypusine synthase in complex with NAD and spermidine
7A6T: “Crystal structure of ASN173SER variant of human deoxyhypusine synthase in complex with NAD and spermidine”. X-ray diffraction, 3 ligands (NAD, SPD, OXM), 8 pockets (best druggability 0.86). MolNFT v1 #172576 on GenesisL1: 3D…
- 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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