Research workbench
Structural basis of cellular dNTP regulation, SAMHD1-GTP-dCTP-cCTP complex
Analyse Structural basis of cellular dNTP regulation, SAMHD1-GTP-dCTP-cCTP complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TNP
- Type
- protein
- Length
- 1,924 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Homo sapiens
- Molecule
- Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
- EC
- 3.1.5.-
- UniProt
- Q9Y3Z3
- Ligands
- DCP, GTP, MG
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · resolution 2 · 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 · 8 copies · chains A, C, D, B
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, C, D, B
- 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 | 934 | 0.89 | 0.91 | 128 | DCP, GTP, MG |
| 2 | 591 | 0.87 | 0.92 | 82 | DCP, GTP |
| 3 | 553 | 0.85 | 0.90 | 86 | DCP, GTP |
| 4 | 147 | 0.82 | 0.98 | 25 | empty |
| 5 | 138 | 0.81 | 0.98 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2166 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 2057 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 1945 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1923 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 552 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4TNP · Structural basis of cellular dntp regulation, SAMHD1-GTP-dctp-cctp complex · the same entry in another collection · chain D against D, TM-score 1.00
- Q9Y3Z3 · AlphaFold monomer V2.0 prediction for deoxynucleoside triphosphate triphosphohydrolase… · a predicted model of the same protein · chain D 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 4TNP · PDBe 4TNP · UniProt Q9Y3Z3
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