Research workbench
SAMHD1 bound to cladribine-tp in the catalytic pocket and allosteric pocket
Analyse SAMHD1 bound to cladribine-tp in the catalytic pocket and allosteric pocket in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DW4
- 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
- HF7, GTP, MG, NA
- 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
- HF7 · 2'-deoxy-2-methyladenosine 5'-(tetrahydrogen triphosphate) · ligand · 8 copies · chains D, C, B, A
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains D, C, A, B
- MG · Magnesium ion · metal · 8 copies · chains D, C, B, A
- NA · Sodium ion · metal · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 982 | 0.89 | 0.91 | 150 | GTP, HF7, MG |
| 2 | 750 | 0.86 | 0.89 | 91 | HF7, MG, GTP |
| 3 | 421 | 0.84 | 0.92 | 70 | HF7 |
| 4 | 162 | 0.83 | 0.98 | 27 | empty |
| 5 | 128 | 0.81 | 0.98 | 27 | empty |
Interfaces
6 interfaces between chains.
- D–B · 2161 Ų buried · 32 hydrogen bonds · protein-protein
- D–A · 1910 Ų buried · 17 hydrogen bonds · protein-protein
- C–B · 1900 Ų buried · 19 hydrogen bonds · protein-protein
- C–A · 1828 Ų buried · 28 hydrogen bonds · protein-protein
- D–C · 540 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6DW4 · SAMHD1 Bound to Cladribine-TP in the Catalytic Pocket and Allosteric Pocket · the same entry in another collection · chain D against D, 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 6DW4 · PDBe 6DW4 · UniProt Q9Y3Z3
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