Research workbench
The structure of GTP-bound SAMHD1
Analyse The structure of GTP-bound SAMHD1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RXO
- Type
- protein
- Length
- 1,767 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
- GTP, ZN, PO4
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 456 | 53% helix, 12% strand | Q9Y3Z3 |
| B | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 433 | 55% helix, 12% strand | Q9Y3Z3 |
| C | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 434 | 55% helix, 12% strand | Q9Y3Z3 |
| D | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 444 | 53% helix, 12% strand | Q9Y3Z3 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 656 | 0.85 | 0.89 | 66 | PO4 |
| 2 | 727 | 0.82 | 0.86 | 73 | PO4 |
| 3 | 140 | 0.82 | 0.98 | 26 | empty |
| 4 | 1107 | 0.81 | 0.82 | 123 | GTP, PO4 |
| 5 | 143 | 0.81 | 0.97 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1876 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1876 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 566 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 498 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 43 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4RXO · The structure of GTP-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 4RXO · PDBe 4RXO · UniProt Q9Y3Z3
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