Research workbench
Human SAMHD1 bound to DEOXYRIBO(C*G*C*C*T)-oligonucleotide
Analyse Human SAMHD1 bound to DEOXYRIBO(C*G*C*C*T)-oligonucleotide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U6X
- Type
- protein + DNA
- Length
- 1,631 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxynucleoside triphosphate triphosphohydrolase SAMHD1; DNA sc-gs-sc-sc-dt
- EC
- 3.1.5.-
- UniProt
- Q9Y3Z3
- Ligands
- SC, ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 56% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 427 | 55% helix, 12% strand | Q9Y3Z3 |
| B | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 383 | 59% helix, 8% strand | Q9Y3Z3 |
| C | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 376 | 58% helix, 9% strand | Q9Y3Z3 |
| D | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 430 | 54% helix, 12% strand | Q9Y3Z3 |
| E, F, H | DNA sc-gs-sc-sc-dt | dna | 4 | — | — |
| G | DNA sc-gs-sc-sc-dt | dna | 3 | — | — |
Ligands and binding sites
- SC · 2-deoxy-cytidine-5'-thiophosphorate · ligand · chains B, C, G
- 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 | 144 | 0.83 | 0.99 | 27 | empty |
| 2 | 131 | 0.81 | 0.99 | 27 | empty |
| 3 | 773 | 0.81 | 0.84 | 73 | ZN |
| 4 | 651 | 0.77 | 0.82 | 57 | ZN |
| 5 | 631 | 0.76 | 0.82 | 62 | ZN |
Interfaces
15 interfaces between chains.
- B–C · 2014 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 1929 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 485 Ų buried · 7 hydrogen bonds · protein-protein
- D–H · 461 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–E · 441 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 15 modified, 2 disulfide, 1 covalent (nucleotide modification, disulfide, covalent ligand).
Compared structures
- 6U6X · Human SAMHD1 bound to deoxyribo(C*G*C*C*T)-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 6U6X · PDBe 6U6X · UniProt Q9Y3Z3
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