MolNFT v1 · #113727 · protein
Crystal structure of human SAMHD1 (amino acid residues 115-583) bound to ddgtp
5AO1 · Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: “Crystal structure of human SAMHD1 (amino acid residues 115-583) bound to ddgtp”. X-ray diffraction, 4 ligands (DG3, FE, MG), 20 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 5AO1
- Type
- protein
- Length
- 1,799 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
- EC
- 3.1.5.-
- UniProt
- Q9Y3Z3
- Ligands
- DG3, FE, MG, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 457 | 52% helix, 12% strand | Q9Y3Z3 |
| B | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 443 | 54% helix, 12% strand | Q9Y3Z3 |
| C | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 457 | 51% helix, 11% strand | Q9Y3Z3 |
| D | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 442 | 54% helix, 12% strand | Q9Y3Z3 |
Ligands and binding sites
- DG3 · 2'-3'-dideoxyguanosine-5'-triphosphate · ligand · 8 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 814 | 0.84 | 0.86 | 83 | FE, DG3 |
| 2 | 840 | 0.82 | 0.85 | 87 | DG3 |
| 3 | 155 | 0.82 | 0.98 | 28 | empty |
| 4 | 124 | 0.80 | 0.98 | 29 | empty |
| 5 | 588 | 0.77 | 0.83 | 62 | DG3 |
Interfaces
6 interfaces between chains.
- C–D · 1920 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1886 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 675 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 503 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 17 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
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 5AO1 · PDBe 5AO1 · UniProt Q9Y3Z3
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