MolNFT v1 · #106745 · protein
Structure basis of cellular dntp regulation, SAMHD1-dgtp-datp- DTTP/DGTP complex
4TO6 · Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: “Structure basis of cellular dntp regulation, SAMHD1-dgtp-datp- DTTP/DGTP complex”. X-ray diffraction, 4 ligands (DGT, DTP, TTP), 20 pockets (best druggability 0.89). MolNFT…
- PDB
- 4TO6
- 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, DTP, TTP, MG
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 53% 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 | 53% helix, 12% strand | Q9Y3Z3 |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 5 copies · chains A, C, D, B
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- TTP · Thymidine-5'-triphosphate · ligand · 3 copies · chains A, B, D
- MG · Magnesium 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1025 | 0.89 | 0.91 | 146 | DGT, DTP, MG |
| 2 | 947 | 0.89 | 0.91 | 134 | DTP, DGT |
| 3 | 148 | 0.82 | 0.98 | 28 | empty |
| 4 | 148 | 0.81 | 0.97 | 27 | empty |
| 5 | 1028 | 0.76 | 0.79 | 72 | TTP |
Interfaces
6 interfaces between chains.
- B–D · 2153 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 2087 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 1927 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1903 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 477 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4TO6 · Structure basis of cellular dNTP regulation, SAMHD1-dGTP-dATP-dTTP/dGTP complex · 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 4TO6 · PDBe 4TO6 · UniProt Q9Y3Z3
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