Research workbench
Structure of sortase a from streptococcus pneumoniae
Analyse Structure of sortase a 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
- 4O8L
- Type
- protein
- Length
- 666 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sortase
- EC
- 3.4.22.70
- UniProt
- Q8DPM3
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sortase (EC 3.4.22.70) | protein | 168 | 20% helix, 35% strand | Q8DPM3 |
| B | Sortase (EC 3.4.22.70) | protein | 156 | 13% helix, 38% strand | Q8DPM3 |
| C | Sortase (EC 3.4.22.70) | protein | 173 | 21% helix, 36% strand | Q8DPM3 |
| D | Sortase (EC 3.4.22.70) | protein | 169 | 17% helix, 37% strand | Q8DPM3 |
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.77 | 0.96 | 26 | empty |
| 2 | 446 | 0.67 | 0.79 | 48 | empty |
| 3 | 305 | 0.57 | 0.77 | 44 | empty |
| 4 | 61 | 0.33 | 0.77 | 17 | empty |
Interfaces
5 interfaces between chains.
- C–D · 5683 Ų buried · 115 hydrogen bonds · protein-protein
- A–B · 5308 Ų buried · 113 hydrogen bonds · protein-protein
- A–C · 369 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 79 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 70 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 4O8L · Structure of sortase A 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 Q8DPM3
- Elsewhere: RCSB PDB 4O8L · PDBe 4O8L · UniProt Q8DPM3
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