Research workbench
Crystal structure of tetrameric human H215A-SAMHD1 (residues 109-626) with rp-dgtp-alphas (T8T) and mg
Analyse Crystal structure of tetrameric human H215A-SAMHD1 (residues 109-626) with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A5Y
- Type
- protein
- Length
- 3,650 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
- EC
- 3.1.5.-
- UniProt
- Q9Y3Z3
- Ligands
- T8T, MG, FE
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 8 distinct chains · 53% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 458 | 52% helix, 14% strand | Q9Y3Z3 |
| B | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 452 | 54% helix, 14% strand | Q9Y3Z3 |
| C | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 459 | 52% helix, 14% strand | Q9Y3Z3 |
| D | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 451 | 54% helix, 14% strand | Q9Y3Z3 |
| E | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 462 | 53% helix, 13% strand | Q9Y3Z3 |
| F | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 455 | 53% helix, 14% strand | Q9Y3Z3 |
| G | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 464 | 52% helix, 13% strand | Q9Y3Z3 |
| H | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 449 | 54% helix, 14% strand | Q9Y3Z3 |
Ligands and binding sites
- T8T · 2'-deoxyguanosine-5'-O-(1-thiotriphosphate) · ligand · 24 copies · chains A, B, C, D, E, F, H, G
- MG · Magnesium ion · metal · 24 copies · chains A, B, C, D, E, G, H, F
- FE · Fe (III) ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 856 | 0.87 | 0.89 | 98 | MG, T8T |
| 2 | 1110 | 0.86 | 0.87 | 125 | MG, T8T |
| 3 | 695 | 0.84 | 0.88 | 82 | T8T, MG |
| 4 | 607 | 0.84 | 0.88 | 79 | MG, T8T |
| 5 | 670 | 0.83 | 0.87 | 80 | MG, T8T |
Interfaces
17 interfaces between chains.
- A–B · 1903 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1900 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1876 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 1862 Ų buried · 22 hydrogen bonds · protein-protein
- F–G · 1629 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 7A5Y · Crystal structure of tetrameric human H215A-SAMHD1 (residues 109-626) with Rp-dGTP-alphaS… · the same entry in another collection · chain D against D, 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 7A5Y · PDBe 7A5Y · UniProt Q9Y3Z3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.