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Crystal structure of tetrameric human D137N-SAMHD1 (residues 109-626) with xtp, dampnpp and mg
Analyse Crystal structure of tetrameric human D137N-SAMHD1 (residues 109-626) with xtp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TX0
- Type
- protein
- Length
- 957 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
- EC
- 3.1.5.-
- UniProt
- Q9Y3Z3
- Ligands
- DZ4, CZF, MG, FE
- Pockets
- 17 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 478 | 53% helix, 13% strand | Q9Y3Z3 |
| B | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 479 | 52% helix, 13% strand | Q9Y3Z3 |
Ligands and binding sites
- DZ4 · 2'-deoxy-5'-O-[(R)-hydroxy{[(r)-hydroxy(phosphonooxy) phosphoryl]amino}phosphoryl]adenosine · ligand · 4 copies · chains A, B
- CZF · [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 6 copies · chains A, B
- FE · Fe (III) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.84 | 0.98 | 28 | empty |
| 2 | 929 | 0.75 | 0.78 | 76 | MG, DZ4 |
| 3 | 915 | 0.74 | 0.78 | 74 | MG, DZ4 |
| 4 | 329 | 0.59 | 0.77 | 34 | empty |
| 5 | 187 | 0.56 | 0.80 | 29 | CZF |
Interfaces
1 interface between chains.
- A–B · 1919 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6TX0 · Crystal structure of tetrameric human D137N-SAMHD1 (residues 109-626) with XTP, dAMPNPP… · 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 6TX0 · PDBe 6TX0 · UniProt Q9Y3Z3
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