Research workbench
Crystal structure of pig SAMHD1
Analyse Crystal structure of pig SAMHD1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YHW
- Type
- protein
- Length
- 3,348 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
- UniProt
- I3LG77
- Ligands
- DGT, MG
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | protein | 453 | 54% helix, 13% strand | I3LG77 |
| B, C | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | protein | 453 | 54% helix, 12% strand | I3LG77 |
| D, E | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | protein | 387 | 53% helix, 12% strand | I3LG77 |
| G, H | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 | protein | 381 | 52% helix, 12% strand | I3LG77 |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 24 copies · chains A, B, D, H, C, F, G, E
- MG · Magnesium ion · metal · 16 copies · chains A, H, B, C, D, E, F, G
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 | 1096 | 0.88 | 0.89 | 128 | DGT, MG |
| 2 | 1083 | 0.88 | 0.89 | 132 | MG, DGT |
| 3 | 743 | 0.86 | 0.90 | 98 | DGT, MG |
| 4 | 686 | 0.86 | 0.90 | 97 | MG, DGT |
| 5 | 150 | 0.83 | 0.99 | 27 | empty |
Interfaces
13 interfaces between chains.
- A–B · 1855 Ų buried · 25 hydrogen bonds · protein-protein
- C–F · 1846 Ų buried · 26 hydrogen bonds · protein-protein
- E–G · 1796 Ų buried · 26 hydrogen bonds · protein-protein
- D–H · 1748 Ų buried · 23 hydrogen bonds · protein-protein
- C–G · 1534 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5YHW · Crystal structure of Pig SAMHD1 · 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 I3LG77
- Elsewhere: RCSB PDB 5YHW · PDBe 5YHW · UniProt I3LG77
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