Research workbench
Structure of human SAMHD1 with non-hydrolysable dgtp analog
Analyse Structure of human SAMHD1 with non-hydrolysable dgtp analog in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UJN
- Type
- protein
- Length
- 1,948 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
- EC
- 3.1.5.-
- UniProt
- Q9Y3Z3
- Ligands
- T8T
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 1 distinct chain · 49% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 487 | 49% helix, 11% strand | Q9Y3Z3 |
Ligands and binding sites
- T8T · 2'-deoxyguanosine-5'-O-(1-thiotriphosphate) · ligand · 12 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 975 | 0.89 | 0.91 | 142 | T8T |
| 2 | 801 | 0.88 | 0.91 | 114 | T8T |
| 3 | 202 | 0.84 | 0.98 | 27 | empty |
| 4 | 200 | 0.84 | 0.97 | 29 | empty |
| 5 | 1095 | 0.76 | 0.79 | 76 | T8T |
Interfaces
6 interfaces between chains.
- A–D · 2167 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 2158 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2030 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 2029 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 464 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 7UJN · Structure of Human SAMHD1 with Non-Hydrolysable dGTP Analog · 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 7UJN · PDBe 7UJN · UniProt Q9Y3Z3
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