Research workbench
Crystal structure of human SAMHD1 (amino acid residues 582-626) bound to vpx isolated from sooty mangabey and human DCAF1 (amino acid residues 1058-1396)
Analyse Crystal structure of human SAMHD1 (amino acid residues 582-626) bound to vpx… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CC9
- Type
- protein
- Length
- 424 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein vprbp; Protein vpx; Deoxynucleoside triphosphate triphosphohydrolase SAMHD1
- EC
- 3.1.5.-
- UniProt
- Q9Y4B6, P19508, Q9Y3Z3
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 18% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein vprbp | protein | 307 | 2% helix, 52% strand | Q9Y4B6 |
| B | Protein vpx | protein | 98 | 62% helix, 1% strand | P19508 |
| C | Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 (EC 3.1.5.-) | protein | 19 | 47% helix, 5% strand | Q9Y3Z3 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1086 | 0.83 | 0.84 | 75 | empty |
| 2 | 187 | 0.60 | 0.82 | 28 | empty |
| 3 | 166 | 0.52 | 0.79 | 27 | empty |
| 4 | 71 | 0.32 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2077 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 740 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 237 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4CC9 · Crystal structure of human SAMHD1 (amino acid residues 582-626) bound to Vpx isolated… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y4B6 · AlphaFold monomer V2.0 prediction for DDB1- and CUL4-associated factor 1 (Q9Y4B6) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9Y4B6
- Every structure of UniProt P19508
- Every structure of UniProt Q9Y3Z3
- Elsewhere: RCSB PDB 4CC9 · PDBe 4CC9 · UniProt Q9Y4B6 · UniProt P19508 · UniProt Q9Y3Z3
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