Research workbench
SAMHD1 Bound to Gemcitabine-TP in the Catalytic Pocket
Analyse SAMHD1 Bound to Gemcitabine-TP in the Catalytic Pocket in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DW5
- Type
- protein
- Length
- 1,910 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.93
- Source
- Homo sapiens
- Molecule
- Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
- EC
- 3.1.5.-
- UniProt
- Q9Y3Z3
- Ligands
- GTF, GTP, DTP, MG, NA, NI
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · resolution 1.93 · 3 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 468 | 52% helix, 13% strand | Q9Y3Z3 |
| B | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 480 | 53% helix, 13% strand | Q9Y3Z3 |
| C, D | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 481 | 52% helix, 13% strand | Q9Y3Z3 |
Ligands and binding sites
- GTF · 2'-deoxy-2',2'-difluorocytidine 5'-(tetrahydrogen triphosphate) · ligand · 4 copies · chains A, B, C, D
- 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 · 10 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C
- NI · Nickel (II) ion · metal · chains B, C
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 | 941 | 0.90 | 0.92 | 136 | GTP, MG, DTP |
| 2 | 833 | 0.88 | 0.91 | 135 | DTP, MG, GTP |
| 3 | 114 | 0.80 | 0.98 | 26 | empty |
| 4 | 116 | 0.80 | 0.98 | 24 | empty |
| 5 | 1049 | 0.77 | 0.79 | 78 | GTF, MG |
Interfaces
6 interfaces between chains.
- B–D · 2138 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1944 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 1932 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1917 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 514 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6DW5 · SAMHD1 bound to gemcitabine-tp in the catalytic pocket · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y3Z3 · AlphaFold monomer V2.0 prediction for deoxynucleoside triphosphate triphosphohydrolase… · a predicted model of the same protein · chain B 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 6DW5 · PDBe 6DW5 · UniProt Q9Y3Z3
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