Research workbench
The structure of GTP-dutp-bound SAMHD1
Analyse The structure of GTP-dutp-bound SAMHD1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RXQ
- Type
- protein
- Length
- 974 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
- DUT, GTP, MG
- Pockets
- 14 · 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 | 51% helix, 13% strand | Q9Y3Z3 |
| B | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 493 | 51% helix, 13% strand | Q9Y3Z3 |
Ligands and binding sites
- DUT · Deoxyuridine-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
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.84 | 0.99 | 26 | empty |
| 2 | 1000 | 0.74 | 0.77 | 71 | DUT |
| 3 | 935 | 0.74 | 0.78 | 72 | DUT |
| 4 | 286 | 0.61 | 0.79 | 39 | GTP, DUT, MG |
| 5 | 341 | 0.61 | 0.78 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1900 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4RXQ · The structure of GTP-dUTP-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 4RXQ · PDBe 4RXQ · UniProt Q9Y3Z3
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