Research workbench
Dutpase from phage PHI11 of S.AUREUS: visualization of the species- specific insert
Analyse Dutpase from phage PHI11 of S.AUREUS: visualization of the species- specific… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4GV8
- Type
- protein
- Length
- 920 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dutpase
- EC
- 3.6.1.23
- UniProt
- Q8SDV3
- Ligands
- DUP, MG
- Pockets
- 7 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 4% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dutpase (EC 3.6.1.23) | protein | 153 | 4% helix, 48% strand | Q8SDV3 |
| B | Dutpase (EC 3.6.1.23) | protein | 154 | 4% helix, 49% strand | Q8SDV3 |
| C, E | Dutpase (EC 3.6.1.23) | protein | 154 | 4% helix, 49% strand | Q8SDV3 |
| D | Dutpase (EC 3.6.1.23) | protein | 152 | 4% helix, 46% strand | Q8SDV3 |
| F | Dutpase (EC 3.6.1.23) | protein | 153 | 4% helix, 49% 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 · 8 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 352 | 0.86 | 0.95 | 53 | empty |
| 2 | 368 | 0.85 | 0.94 | 58 | empty |
| 3 | 879 | 0.78 | 0.81 | 106 | DUP, MG |
| 4 | 179 | 0.60 | 0.82 | 25 | DUP, MG |
| 5 | 166 | 0.57 | 0.82 | 30 | DUP, MG |
Interfaces
10 interfaces between chains.
- B–C · 1715 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1697 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1671 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 1654 Ų buried · 27 hydrogen bonds · protein-protein
- D–F · 1625 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 4GV8 · DUTPase from phage phi11 of S.aureus: visualization of the species-specific insert · the same entry in another collection · chain C against C, 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 4GV8 · PDBe 4GV8 · UniProt Q8SDV3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.