Research workbench
X-ray structure of DNA processing protein a (dpra) from streptococcus pneumoniae
Analyse X-ray structure of DNA processing protein a (dpra) from streptococcus pneumoniae in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UQZ
- Type
- protein
- Length
- 845 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA processing protein dpra
- UniProt
- Q97QF0
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA processing protein dpra | protein | 283 | 47% helix, 14% strand | Q97QF0 |
| B | DNA processing protein dpra | protein | 280 | 48% helix, 14% strand | Q97QF0 |
| C | DNA processing protein dpra | protein | 282 | 47% helix, 14% strand | Q97QF0 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 768 | 0.82 | 0.85 | 86 | SO4 |
| 2 | 237 | 0.62 | 0.81 | 34 | empty |
| 3 | 172 | 0.61 | 0.83 | 23 | empty |
| 4 | 96 | 0.59 | 0.87 | 18 | empty |
| 5 | 231 | 0.58 | 0.79 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1053 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 363 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 237 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 15 modified (engineered).
Compared structures
- 3UQZ · X-ray structure of DNA processing protein A (DprA) from Streptococcus pneumoniae · 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 Q97QF0
- Elsewhere: RCSB PDB 3UQZ · PDBe 3UQZ · UniProt Q97QF0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.