Research workbench
SAMHD1(113-626) H206R D207N R366C
Analyse SAMHD1(113-626) H206R D207N R366C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LTT
- 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
- DGT, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 53% 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 | 53% helix, 13% strand | Q9Y3Z3 |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 8 copies · chains A, C, D, B
- MG · Magnesium 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 933 | 0.87 | 0.89 | 117 | MG, DGT |
| 2 | 769 | 0.86 | 0.89 | 99 | DGT, MG |
| 3 | 739 | 0.85 | 0.89 | 81 | DGT, MG |
| 4 | 686 | 0.85 | 0.88 | 85 | MG, DGT |
| 5 | 141 | 0.82 | 0.99 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2113 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 2006 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 1922 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1904 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 582 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7LTT · SAMHD1(113-626) H206R D207N R366C · 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 7LTT · PDBe 7LTT · UniProt Q9Y3Z3
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