MolNFT v1 · #100492 · protein
Structural insight into dgtp-dependent activation of tetrameric SAMHD1 deoxynucleoside triphosphate triphosphohydrolase
4MZ7 · Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: “Structural insight into dgtp-dependent activation of tetrameric SAMHD1 deoxynucleoside triphosphate…”. X-ray diffraction, 4 ligands (DGT, DTP, ZN), 14 pockets (best…
- PDB
- 4MZ7
- 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
- DGT, DTP, ZN, MG
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 481 | 52% helix, 13% strand | Q9Y3Z3 |
| B | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 493 | 51% helix, 14% strand | Q9Y3Z3 |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 5 copies · chains A, B
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains A, B
- ZN · Zinc ion · metal · 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 | 166 | 0.84 | 0.99 | 28 | empty |
| 2 | 1025 | 0.75 | 0.78 | 84 | DGT |
| 3 | 954 | 0.75 | 0.78 | 73 | DGT |
| 4 | 383 | 0.62 | 0.77 | 32 | empty |
| 5 | 349 | 0.62 | 0.78 | 42 | DGT, MG, DTP |
Interfaces
1 interface between chains.
- A–B · 1898 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4MZ7 · Structural insight into dGTP-dependent activation of tetrameric SAMHD1 deoxynucleoside… · 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 4MZ7 · PDBe 4MZ7 · UniProt Q9Y3Z3
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