MolNFT v1 · #113728 · protein
Crystal structure of human SAMHD1 (amino acid residues 115-583) R164A variant bound to dgtp
5AO2 · Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: “Crystal structure of human SAMHD1 (amino acid residues 115-583) R164A variant bound to dgtp”. X-ray diffraction, 2 ligands (DGT, FE), 20 pockets (best druggability 0.84).…
- PDB
- 5AO2
- Type
- protein
- Length
- 1,711 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
- DGT, FE
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 436 | 53% helix, 12% strand | Q9Y3Z3 |
| B, D | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 419 | 56% helix, 11% strand | Q9Y3Z3 |
| C | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 437 | 54% helix, 12% strand | Q9Y3Z3 |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.84 | 0.98 | 27 | empty |
| 2 | 201 | 0.84 | 0.97 | 27 | empty |
| 3 | 958 | 0.82 | 0.84 | 97 | empty |
| 4 | 622 | 0.77 | 0.83 | 59 | empty |
| 5 | 578 | 0.76 | 0.83 | 50 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1948 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1905 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 563 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 345 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5AO2 · Crystal structure of human SAMHD1 (amino acid residues 115-583) R164A variant bound to… · 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 5AO2 · PDBe 5AO2 · UniProt Q9Y3Z3
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