MolNFT v1 · #165800 · protein + RNA
Human SAMHD1 bound to RIBO(CGCCU)-oligonucleotide
6U6Y · Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: “Human SAMHD1 bound to RIBO(CGCCU)-oligonucleotide”. X-ray diffraction, 2 ligands (DTP, ZN), 20 pockets (best druggability 0.83). MolNFT v1 #165800 on GenesisL1: 3D structure…
- PDB
- 6U6Y
- Type
- protein + RNA
- Length
- 1,744 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxynucleoside triphosphate triphosphohydrolase SAMHD1; RNA cgccu
- EC
- 3.1.5.-
- UniProt
- Q9Y3Z3
- Ligands
- DTP, ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 434 | 54% helix, 13% strand | Q9Y3Z3 |
| B | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 437 | 54% helix, 12% strand | Q9Y3Z3 |
| C | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 431 | 54% helix, 12% strand | Q9Y3Z3 |
| D | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 430 | 55% helix, 12% strand | Q9Y3Z3 |
| E, G, F, H | RNA cgccu | rna | 3 | — | — |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.83 | 0.99 | 29 | empty |
| 2 | 146 | 0.82 | 0.98 | 28 | empty |
| 3 | 584 | 0.80 | 0.86 | 55 | ZN, DTP |
| 4 | 1049 | 0.79 | 0.81 | 97 | empty |
| 5 | 690 | 0.77 | 0.82 | 54 | ZN, DTP |
Interfaces
16 interfaces between chains.
- B–C · 1890 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1887 Ų buried · 20 hydrogen bonds · protein-protein
- B–D · 551 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 525 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 310 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 6U6Y · Human SAMHD1 bound to ribo(CGCCU)-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 6U6Y · PDBe 6U6Y · UniProt Q9Y3Z3
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