Research workbench
The 3D structure of D95N mutant dutpase from phage PHI11 of S. aureus reveals the molecular details for the coordination of a structural MG(II) ion
Analyse The 3D structure of D95N mutant dutpase from phage PHI11 of S. aureus reveals… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WRK
- Type
- protein
- Length
- 927 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dutpase
- UniProt
- Q8SDV3
- Ligands
- DUP, MG
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 4% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dutpase | protein | 158 | 4% helix, 46% strand | Q8SDV3 |
| B | Dutpase | protein | 155 | 4% helix, 47% strand | Q8SDV3 |
| C, D | Dutpase | protein | 153 | 4% helix, 49% strand | Q8SDV3 |
| E | Dutpase | protein | 153 | 6% helix, 48% strand | Q8SDV3 |
| F | Dutpase | protein | 155 | 4% helix, 46% strand | Q8SDV3 |
Ligands and binding sites
- DUP · 2'-deoxyuridine 5'-alpha,beta-imido-triphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 443 | 0.85 | 0.92 | 58 | empty |
| 2 | 464 | 0.84 | 0.91 | 58 | empty |
| 3 | 927 | 0.74 | 0.78 | 90 | DUP, MG |
| 4 | 218 | 0.63 | 0.82 | 32 | DUP, MG |
| 5 | 184 | 0.60 | 0.83 | 29 | DUP, MG |
Interfaces
9 interfaces between chains.
- E–F · 1737 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1684 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1661 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 1552 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1547 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 4WRK · The 3D structure of D95N mutant DUTPase from phage phi11 of S. aureus reveals the… · 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 Q8SDV3
- Elsewhere: RCSB PDB 4WRK · PDBe 4WRK · UniProt Q8SDV3
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