MolNFT v1 · #112803 · protein
Crystal structure of the dgtp-bound catalytic core of SAMHD1 T592V mutant
4ZWE · Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: “Crystal structure of the dgtp-bound catalytic core of SAMHD1 T592V mutant”. X-ray diffraction, 2 ligands (DGT, MG), 20 pockets (best druggability 0.88). MolNFT v1 #112803 on…
- PDB
- 4ZWE
- Type
- protein
- Length
- 1,920 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
- DGT, MG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 480 | 52% helix, 12% strand | Q9Y3Z3 |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 12 copies · chains A, C, D, B
- MG · Magnesium ion · metal · 5 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 | 691 | 0.88 | 0.93 | 84 | DGT |
| 2 | 702 | 0.88 | 0.93 | 78 | empty |
| 3 | 184 | 0.83 | 0.98 | 27 | empty |
| 4 | 177 | 0.83 | 0.98 | 28 | empty |
| 5 | 963 | 0.75 | 0.78 | 76 | DGT, MG |
Interfaces
6 interfaces between chains.
- A–C · 1993 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 1950 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1890 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1870 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 490 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4ZWE · Crystal structure of the dGTP-bound catalytic core of SAMHD1 T592V mutant · 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 4ZWE · PDBe 4ZWE · UniProt Q9Y3Z3
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