MolNFT v1 · #126962 · protein
Pirating conserved phage mechanisms promotes promiscuous staphylococcal pathogenicity islands transfer.
5MIL · Dutpase family protein: “Pirating conserved phage mechanisms promotes promiscuous staphylococcal pathogenicity islands transfer.”. X-ray diffraction, 2 ligands (DUP, MG), 6 pockets (best druggability 0.62). MolNFT v1 #126962 on…
- PDB
- 5MIL
- Type
- protein
- Length
- 313 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dutpase family protein
- UniProt
- A0A163S774
- Ligands
- DUP, MG
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dutpase family protein | protein | 157 | 72% helix, 0% strand | A0A163S774 |
| B | Dutpase family protein | protein | 156 | 71% helix, 0% strand | A0A163S774 |
Ligands and binding sites
- DUP · 2'-deoxyuridine 5'-alpha,beta-imido-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.62 | 0.83 | 28 | DUP, MG |
| 2 | 54 | 0.62 | 0.93 | 19 | empty |
| 3 | 156 | 0.61 | 0.84 | 25 | DUP, MG |
| 4 | 122 | 0.47 | 0.78 | 21 | empty |
| 5 | 92 | 0.45 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1225 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5MIL · Pirating conserved phage mechanisms promotes promiscuous staphylococcal pathogenicity… · 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 A0A163S774
- Elsewhere: RCSB PDB 5MIL · PDBe 5MIL · UniProt A0A163S774
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