MolNFT v1 · #113726 · protein
Crystal structure of human SAMHD1 (amino acid residues 41-583) bound to ddgtp
5AO0 · Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: “Crystal structure of human SAMHD1 (amino acid residues 41-583) bound to ddgtp”. X-ray diffraction, 3 ligands (DG3, FE, MG), 14 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 5AO0
- Type
- protein
- Length
- 874 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
- UniProt
- Q9Y3Z3
- Ligands
- DG3, FE, MG
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | protein | 439 | 54% helix, 13% strand | Q9Y3Z3 |
| B | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | protein | 435 | 54% helix, 11% strand | Q9Y3Z3 |
Ligands and binding sites
- DG3 · 2'-3'-dideoxyguanosine-5'-triphosphate · ligand · 4 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.83 | 0.98 | 26 | empty |
| 2 | 620 | 0.75 | 0.81 | 55 | DG3 |
| 3 | 556 | 0.73 | 0.81 | 59 | FE, DG3 |
| 4 | 217 | 0.62 | 0.82 | 35 | empty |
| 5 | 359 | 0.61 | 0.77 | 35 | empty |
Interfaces
1 interface between chains.
- A–B · 1901 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5AO0 · Crystal structure of human SAMHD1 (amino acid residues 41-583) bound to ddGTP · the same entry in another collection · chain A 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 Q9Y3Z3
- Elsewhere: RCSB PDB 5AO0 · PDBe 5AO0 · UniProt Q9Y3Z3
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