Research workbench
Crystal structure of in vitro phosphorylated human SAMHD1 (amino acid residues 115-626) bound to GTP
Analyse Crystal structure of in vitro phosphorylated human SAMHD1 (amino acid residues… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AO4
- Type
- protein
- Length
- 1,625 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, FE
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 430 | 52% helix, 12% strand | Q9Y3Z3 |
| B | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 422 | 54% helix, 12% strand | Q9Y3Z3 |
| C | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 389 | 53% helix, 12% strand | Q9Y3Z3 |
| D | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 384 | 57% helix, 8% strand | Q9Y3Z3 |
Ligands and binding sites
- GTP · Guanosine-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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 248 | 0.84 | 0.96 | 30 | empty |
| 2 | 129 | 0.81 | 0.98 | 25 | empty |
| 3 | 1165 | 0.76 | 0.79 | 113 | FE, GTP |
| 4 | 560 | 0.73 | 0.81 | 51 | empty |
| 5 | 561 | 0.73 | 0.81 | 58 | FE |
Interfaces
6 interfaces between chains.
- A–B · 1897 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1745 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 419 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 172 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 110 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5AO4 · Crystal structure of in vitro phosphorylated human SAMHD1 (amino acid residues 115-626)… · 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 5AO4 · PDBe 5AO4 · UniProt Q9Y3Z3
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