MolNFT v1 · #106739 · protein
Structure basis of cellular dntp regulation, SAMHD1-GTP-datp-dctp complex
4TO0 · Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: “Structure basis of cellular dntp regulation, SAMHD1-GTP-datp-dctp complex”. X-ray diffraction, 4 ligands (DCP, GTP, DTP), 20 pockets (best druggability 0.89). MolNFT v1…
- PDB
- 4TO0
- Type
- protein
- Length
- 1,924 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, DTP, MG
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 479 | 53% helix, 13% strand | Q9Y3Z3 |
| B | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 480 | 53% helix, 13% strand | Q9Y3Z3 |
| C | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 481 | 52% 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
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 4 copies · chains A, B, C, 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1082 | 0.89 | 0.91 | 145 | GTP, DTP |
| 2 | 909 | 0.89 | 0.92 | 124 | DTP, GTP |
| 3 | 145 | 0.82 | 0.98 | 26 | empty |
| 4 | 145 | 0.81 | 0.97 | 26 | empty |
| 5 | 961 | 0.76 | 0.79 | 72 | DCP |
Interfaces
6 interfaces between chains.
- A–C · 2175 Ų buried · 38 hydrogen bonds · protein-protein
- B–D · 2049 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 1944 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1924 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 540 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4TO0 · Structure basis of cellular dNTP regulation, SAMHD1-GTP-dATP-dCTP 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 4TO0 · PDBe 4TO0 · UniProt Q9Y3Z3
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