Research workbench
Structure basis of cellular dntp regulation, SAMHD1-GTP-dttp-dctp complex
Analyse Structure basis of cellular dntp regulation, SAMHD1-GTP-dttp-dctp complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TO5
- Type
- protein
- Length
- 1,919 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
- DCP, GTP, TTP, MG
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 4 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 | 53% helix, 13% strand | Q9Y3Z3 |
| C | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 479 | 52% helix, 13% strand | Q9Y3Z3 |
| D | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 480 | 53% helix, 13% strand | Q9Y3Z3 |
| B | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 480 | 52% helix, 13% strand | Q9Y3Z3 |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · 4 copies · chains A, C, D, B
- GTP · Guanosine-5'-triphosphate · ligand · 4 copies · chains A, C, D, B
- TTP · Thymidine-5'-triphosphate · ligand · 4 copies · chains A, C, B, 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 996 | 0.90 | 0.91 | 144 | GTP, TTP |
| 2 | 1013 | 0.90 | 0.91 | 137 | GTP, TTP |
| 3 | 139 | 0.81 | 0.98 | 26 | empty |
| 4 | 134 | 0.81 | 0.98 | 28 | empty |
| 5 | 1021 | 0.76 | 0.78 | 79 | DCP |
Interfaces
6 interfaces between chains.
- A–C · 2070 Ų buried · 26 hydrogen bonds · protein-protein
- D–B · 2052 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 1945 Ų buried · 27 hydrogen bonds · protein-protein
- C–B · 1939 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 571 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4TO5 · Structure basis of cellular dNTP regulation, SAMHD1-GTP-dTTP-dCTP complex · 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 4TO5 · PDBe 4TO5 · UniProt Q9Y3Z3
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