Research workbench
Structure basis of cellular dntp regulation, SAMHD1-GTP-dgtp complex
Analyse Structure basis of cellular dntp regulation, SAMHD1-GTP-dgtp complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TNX
- 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
- DGT, GTP, 3PO, MG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 481 | 52% helix, 14% strand | Q9Y3Z3 |
| B | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 479 | 52% helix, 13% strand | Q9Y3Z3 |
| D | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 483 | 52% helix, 13% strand | Q9Y3Z3 |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 4 copies · chains A, C, D, B
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, C, D, B
- 3PO · Triphosphate · ligand · chains A
- 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 797 | 0.88 | 0.91 | 116 | DGT |
| 2 | 644 | 0.85 | 0.89 | 80 | MG, DGT, GTP |
| 3 | 530 | 0.85 | 0.91 | 82 | DGT, GTP, MG |
| 4 | 140 | 0.82 | 0.98 | 27 | empty |
| 5 | 142 | 0.82 | 0.98 | 27 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2142 Ų buried · 34 hydrogen bonds · protein-protein
- A–C · 2089 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 1927 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1917 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 491 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4TNX · Structure basis of cellular dNTP regulation, SAMHD1-GTP-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 4TNX · PDBe 4TNX · UniProt Q9Y3Z3
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