MolNFT v1 · #146907 · protein
SAMHD1 bound to vidarabine-tp in the catalytic pocket
6DWJ · Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: “SAMHD1 bound to vidarabine-tp in the catalytic pocket”. X-ray diffraction, 7 ligands (HEJ, GTP, DTP), 20 pockets (best druggability 0.89). MolNFT v1 #146907 on GenesisL1: 3D…
- PDB
- 6DWJ
- Type
- protein
- Length
- 1,924 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
- HEJ, GTP, DTP, GLY, NA, MG, PO4
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, C, B, A | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 481 | 53% helix, 13% strand | Q9Y3Z3 |
Ligands and binding sites
- HEJ · 9-{5-O-[(S)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}-9H-purin-6-amine · ligand · 4 copies · chains D, C, B, A
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains D, B, A, C
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 4 copies · chains D, C, B, A
- GLY · Glycine · ligand · chains D, B
- NA · Sodium ion · metal · 17 copies · chains D, A, C, B
- MG · Magnesium ion · metal · 10 copies · chains D, C, B, A
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1008 | 0.89 | 0.91 | 141 | MG, GTP, DTP |
| 2 | 1091 | 0.89 | 0.91 | 157 | GTP, DTP, MG, NA, GLY |
| 3 | 130 | 0.82 | 0.99 | 25 | empty |
| 4 | 136 | 0.81 | 0.98 | 25 | empty |
| 5 | 937 | 0.75 | 0.78 | 73 | HEJ, MG |
Interfaces
6 interfaces between chains.
- C–A · 2220 Ų buried · 26 hydrogen bonds · protein-protein
- D–B · 2163 Ų buried · 22 hydrogen bonds · protein-protein
- C–B · 1941 Ų buried · 19 hydrogen bonds · protein-protein
- D–A · 1936 Ų buried · 19 hydrogen bonds · protein-protein
- D–C · 543 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6DWJ · SAMHD1 Bound to Vidarabine-TP in the Catalytic Pocket · the same entry in another collection · chain B against B, TM-score 1.00
- Q9Y3Z3 · AlphaFold monomer V2.0 prediction for deoxynucleoside triphosphate triphosphohydrolase… · a predicted model of the same protein · chain B 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 6DWJ · PDBe 6DWJ · UniProt Q9Y3Z3
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