Research workbench
Structure basis of cellular dntp regulation, SAMHD1-GTP-datp-datp complex
Analyse Structure basis of cellular dntp regulation, SAMHD1-GTP-datp-datp complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TNR
- 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 · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, C, B, A | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 481 | 52% helix, 13% strand | Q9Y3Z3 |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 7 copies · chains D, C, B, A
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains D, B, A, C
- MG · Magnesium ion · metal · 4 copies · chains D, C, B, A
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 | 1132 | 0.89 | 0.91 | 152 | GTP, DTP, MG |
| 2 | 1192 | 0.89 | 0.91 | 162 | MG, DTP, GTP |
| 3 | 166 | 0.83 | 0.98 | 28 | empty |
| 4 | 151 | 0.82 | 0.98 | 28 | empty |
| 5 | 1023 | 0.75 | 0.78 | 77 | DTP |
Interfaces
6 interfaces between chains.
- C–A · 2122 Ų buried · 31 hydrogen bonds · protein-protein
- D–B · 2118 Ų buried · 30 hydrogen bonds · protein-protein
- D–A · 1955 Ų buried · 24 hydrogen bonds · protein-protein
- C–B · 1921 Ų buried · 18 hydrogen bonds · protein-protein
- B–A · 487 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4TNR · Structure basis of cellular dNTP regulation, SAMHD1-GTP-dATP-dATP complex · the same entry in another collection · chain D against D, 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 4TNR · PDBe 4TNR · UniProt Q9Y3Z3
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