Research workbench
The structure of GTP-dttp-bound SAMHD1
Analyse The structure of GTP-dttp-bound SAMHD1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RXS
- Type
- protein
- Length
- 973 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
- EC
- 3.1.5.-
- UniProt
- Q9Y3Z3
- Ligands
- TTP, GTP, MG
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 481 | 52% helix, 12% strand | Q9Y3Z3 |
| B | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 492 | 50% helix, 13% strand | Q9Y3Z3 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · 4 copies · chains A, B
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.84 | 0.99 | 26 | empty |
| 2 | 989 | 0.75 | 0.78 | 75 | TTP |
| 3 | 1065 | 0.74 | 0.77 | 88 | TTP |
| 4 | 347 | 0.62 | 0.78 | 33 | empty |
| 5 | 345 | 0.61 | 0.78 | 39 | GTP, MG, TTP |
Interfaces
1 interface between chains.
- A–B · 1912 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 4RXS · The structure of GTP-dTTP-bound SAMHD1 · 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 4RXS · PDBe 4RXS · UniProt Q9Y3Z3
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