Research workbench
Crystal structure of the tetrameric GTP/DATP-bound SAMHD1 (RN206) mutant catalytic core
Analyse Crystal structure of the tetrameric GTP/DATP-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
- 4QG1
- 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
- DTP, GTP, 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
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 8 copies · chains A, B, C, D
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains B, C, D, A
- 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1087 | 0.89 | 0.91 | 151 | GTP, DTP, MG |
| 2 | 753 | 0.86 | 0.89 | 97 | DTP, GTP, MG |
| 3 | 556 | 0.85 | 0.91 | 79 | DTP, MG, GTP |
| 4 | 172 | 0.83 | 0.98 | 28 | empty |
| 5 | 135 | 0.81 | 0.98 | 26 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2111 Ų buried · 33 hydrogen bonds · protein-protein
- A–C · 2105 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 1969 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 1929 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 487 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4QG1 · Crystal structure of the tetrameric GTP/dATP-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 4QG1 · PDBe 4QG1 · UniProt Q9Y3Z3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.