Research workbench
Structure basis of cellular dntp regulation, SAMHD1-GTP-dgtp-dctp complex
Analyse Structure basis of cellular dntp regulation, SAMHD1-GTP-dgtp-dctp complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TO4
- Type
- protein
- Length
- 1,927 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
- DCP, GTP, DGT, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 481 | 53% helix, 13% strand | Q9Y3Z3 |
| D | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 484 | 52% helix, 13% strand | Q9Y3Z3 |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, C, D, B
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 8 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 | 824 | 0.87 | 0.89 | 88 | MG, DGT, GTP |
| 2 | 705 | 0.86 | 0.90 | 91 | GTP, DGT, MG |
| 3 | 794 | 0.86 | 0.89 | 90 | GTP, MG, DGT |
| 4 | 586 | 0.84 | 0.89 | 75 | DGT, MG |
| 5 | 135 | 0.81 | 0.98 | 26 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2081 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 2034 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 1934 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1917 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 519 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4TO4 · Structure basis of cellular dNTP regulation, SAMHD1-GTP-dGTP-dCTP complex · the same entry in another collection · chain C against C, 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 4TO4 · PDBe 4TO4 · UniProt Q9Y3Z3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.