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Crystal structure of the tetrameric DGTP/DUTP-bound SAMHD1 (RN206) mutant catalytic core
Analyse Crystal structure of the tetrameric DGTP/DUTP-bound SAMHD1 (RN206) mutant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QG0
- Type
- protein
- Length
- 1,923 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
- DUT, DGT, MG
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 481 | 52% helix, 13% strand | Q9Y3Z3 |
| B | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 480 | 52% helix, 13% strand | Q9Y3Z3 |
Ligands and binding sites
- DUT · Deoxyuridine-5'-triphosphate · ligand · 8 copies · chains A, B, C, D
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 4 copies · chains A, C, D, B
- MG · Magnesium ion · metal · 7 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · chains 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1009 | 0.90 | 0.92 | 147 | DGT, DUT, MG |
| 2 | 772 | 0.86 | 0.89 | 102 | DGT, MG, DUT |
| 3 | 174 | 0.84 | 0.98 | 29 | empty |
| 4 | 1148 | 0.83 | 0.84 | 97 | MG, DUT, DGT |
| 5 | 159 | 0.83 | 0.98 | 26 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2191 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 2191 Ų buried · 34 hydrogen bonds · protein-protein
- A–D · 1890 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1885 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 552 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4QG0 · Crystal structure of the tetrameric dGTP/dUTP-bound SAMHD1 (RN206) mutant catalytic core · 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 4QG0 · PDBe 4QG0 · UniProt Q9Y3Z3
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