MolNFT v1 · #104612 · protein
Crystal structure of the tetrameric DGTP/DCTP-bound SAMHD1 (RN206) mutant catalytic core
4QFY · Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: “Crystal structure of the tetrameric DGTP/DCTP-bound SAMHD1 (RN206) mutant catalytic core”. X-ray diffraction, 3 ligands (DGT, DCP, MG), 20 pockets (best druggability 0.89).…
- PDB
- 4QFY
- 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
- DGT, DCP, MG
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 480 | 52% helix, 12% strand | Q9Y3Z3 |
| B, C, D | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 481 | 52% helix, 13% strand | Q9Y3Z3 |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 8 copies · chains A, C, D, B
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 986 | 0.89 | 0.91 | 141 | DGT, MG |
| 2 | 766 | 0.86 | 0.89 | 89 | DGT, MG |
| 3 | 705 | 0.85 | 0.89 | 74 | DGT, MG |
| 4 | 152 | 0.82 | 0.98 | 27 | empty |
| 5 | 137 | 0.81 | 0.98 | 28 | empty |
Interfaces
6 interfaces between chains.
- A–C · 2180 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 2160 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 1918 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1916 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 490 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4QFY · Crystal structure of the tetrameric dGTP/dCTP-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 4QFY · PDBe 4QFY · UniProt Q9Y3Z3
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