MolNFT v1 · #113563 · protein
Crystal structure of mandrill SAMHD1 (amino acid residues 1-114) bound to vpx isolated from mandrill and human DCAF1 (amino acid residues 1058-1396)
5AJA · Protein vprbp: “Crystal structure of mandrill SAMHD1 (amino acid residues 1-114) bound to vpx isolated from mandrill and…”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.83). MolNFT v1 #113563 on GenesisL1: 3D…
- PDB
- 5AJA
- Type
- protein
- Length
- 485 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein vprbp; Vpx protein; SAM domain and hd domain-containing protein
- EC
- 2.7.11.1
- UniProt
- Q9Y4B6, Q7ZB17, H6WEA4
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein vprbp (EC 2.7.11.1) | protein | 307 | 1% helix, 50% strand | Q9Y4B6 |
| B | Vpx protein | protein | 84 | 68% helix, 2% strand | Q7ZB17 |
| C | SAM domain and hd domain-containing protein | protein | 94 | 49% helix, 1% strand | H6WEA4 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1150 | 0.83 | 0.84 | 84 | empty |
| 2 | 184 | 0.55 | 0.79 | 22 | empty |
| 3 | 60 | 0.51 | 0.86 | 17 | empty |
| 4 | 56 | 0.45 | 0.84 | 19 | empty |
| 5 | 91 | 0.40 | 0.77 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1730 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 1480 Ų buried · 25 hydrogen bonds · protein-protein
- A–C · 589 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5AJA · Crystal structure of mandrill SAMHD1 (amino acid residues 1-114) 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 Q7ZB17
- Every structure of UniProt H6WEA4
- Elsewhere: RCSB PDB 5AJA · PDBe 5AJA · UniProt Q9Y4B6 · UniProt Q7ZB17 · UniProt H6WEA4
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