MolNFT v1 · #106738 · protein
Structure basis of cellular dntp regulation, SAMHD1-GTP-datp-dttp complex
4TNZ · Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: “Structure basis of cellular dntp regulation, SAMHD1-GTP-datp-dttp complex”. X-ray diffraction, 4 ligands (TTP, GTP, DTP), 20 pockets (best druggability 0.90). MolNFT v1…
- PDB
- 4TNZ
- Type
- protein
- Length
- 1,922 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
- TTP, GTP, DTP, MG
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, B | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 481 | 52% helix, 13% strand | Q9Y3Z3 |
| A | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 480 | 53% helix, 13% strand | Q9Y3Z3 |
| D | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 480 | 53% helix, 12% strand | Q9Y3Z3 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · 4 copies · chains C, A, D, B
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains C, A, B, D
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 4 copies · chains C, A, D, B
- MG · Magnesium ion · metal · 8 copies · chains C, D, A, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.90 | 0.91 | 150 | GTP, DTP, MG |
| 2 | 1116 | 0.89 | 0.91 | 154 | MG, GTP, DTP |
| 3 | 154 | 0.83 | 0.98 | 28 | empty |
| 4 | 166 | 0.82 | 0.97 | 27 | empty |
| 5 | 1029 | 0.76 | 0.79 | 70 | TTP, MG |
Interfaces
6 interfaces between chains.
- C–A · 2170 Ų buried · 29 hydrogen bonds · protein-protein
- D–B · 2151 Ų buried · 28 hydrogen bonds · protein-protein
- C–B · 1931 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 1895 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 463 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4TNZ · Structure basis of cellular dNTP regulation, SAMHD1-GTP-dATP-dTTP 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 4TNZ · PDBe 4TNZ · UniProt Q9Y3Z3
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