Research workbench
Human SAMHD1 bound to DEOXYRIBO(TG*TTCA)-oligonucleotide
Analyse Human SAMHD1 bound to DEOXYRIBO(TG*TTCA)-oligonucleotide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U6Z
- Type
- protein + DNA
- Length
- 1,738 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxynucleoside triphosphate triphosphohydrolase SAMHD1; DNA polymer TG(PST)TCA
- EC
- 3.1.5.-
- UniProt
- Q9Y3Z3
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 55% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 442 | 53% helix, 12% strand | Q9Y3Z3 |
| B | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 429 | 55% helix, 13% strand | Q9Y3Z3 |
| C | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 438 | 54% helix, 13% strand | Q9Y3Z3 |
| D | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 420 | 56% helix, 11% strand | Q9Y3Z3 |
| E, F, H | DNA polymer TG(PST)TCA | dna | 2 | — | — |
| G | DNA polymer TG(PST)TCA | dna | 3 | — | — |
Ligands and binding sites
- ZN · Zinc 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 153 | 0.83 | 0.99 | 28 | empty |
| 2 | 133 | 0.81 | 0.98 | 28 | empty |
| 3 | 630 | 0.79 | 0.84 | 52 | empty |
| 4 | 782 | 0.79 | 0.82 | 73 | empty |
| 5 | 553 | 0.78 | 0.85 | 55 | empty |
Interfaces
11 interfaces between chains.
- B–C · 1918 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1893 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 600 Ų buried · 10 hydrogen bonds · protein-protein
- B–G · 274 Ų buried · 7 hydrogen bonds · protein-nucleic
- C–F · 273 Ų buried · 6 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 6U6Z · Human SAMHD1 bound to deoxyribo(TG*TTCA)-oligonucleotide · 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 6U6Z · PDBe 6U6Z · UniProt Q9Y3Z3
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