MolNFT v1 · #104616 · protein
Crystal structure of the tetrameric GTP/DATP/ATP-bound SAMHD1 (RN206) mutant catalytic core
4QG2 · Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: “Crystal structure of the tetrameric GTP/DATP/ATP-bound SAMHD1 (RN206) mutant catalytic core”. X-ray diffraction, 3 ligands (GTP, DTP, MG), 20 pockets (best druggability…
- PDB
- 4QG2
- 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
- GTP, DTP, MG
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 481 | 51% helix, 12% strand | Q9Y3Z3 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, C, D, B
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- 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 | 1200 | 0.89 | 0.91 | 157 | GTP, DTP, MG |
| 2 | 640 | 0.85 | 0.90 | 77 | GTP, MG, DTP |
| 3 | 1067 | 0.84 | 0.85 | 94 | MG, DTP, GTP |
| 4 | 168 | 0.83 | 0.98 | 28 | empty |
| 5 | 172 | 0.83 | 0.98 | 28 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2156 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 2137 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 1921 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1920 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 451 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4QG2 · Crystal structure of the tetrameric GTP/dATP/ATP-bound SAMHD1 (RN206) mutant catalytic… · 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 4QG2 · PDBe 4QG2 · UniProt Q9Y3Z3
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