Research workbench
SAMHD1 hd domain bound to cndac
Analyse SAMHD1 hd domain bound to cndac in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S2Y
- Type
- protein
- Length
- 1,924 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
- EC
- 3.1.5.-
- UniProt
- Q9Y3Z3
- Ligands
- 85T, DTP, GTP, MG
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 481 | 52% helix, 13% strand | Q9Y3Z3 |
Ligands and binding sites
- 85T · 4-amino-1-{2-cyano-2-deoxy-5-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-arabinofuranosyl}pyrimidin-2(1H)-one · ligand · 4 copies · chains A, B, C, D
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains B, C, D, A
- MG · Magnesium ion · metal · 8 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 921 | 0.89 | 0.92 | 133 | DTP, GTP |
| 2 | 881 | 0.89 | 0.92 | 135 | DTP, GTP |
| 3 | 158 | 0.83 | 0.98 | 27 | empty |
| 4 | 144 | 0.82 | 0.99 | 26 | empty |
| 5 | 955 | 0.76 | 0.79 | 77 | 85T, MG |
Interfaces
6 interfaces between chains.
- A–C · 2211 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 2184 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1925 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 1925 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 510 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7S2Y · SAMHD1 HD domain bound to CNDAC · the same entry in another collection · chain B against B, 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 7S2Y · PDBe 7S2Y · UniProt Q9Y3Z3
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