Research workbench
The crystal structure of the complex of streptococcus agalactiae sortase C1 and mtset
Analyse The crystal structure of the complex of streptococcus agalactiae sortase C1 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TBE
- Type
- protein
- Length
- 1,150 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sortase family protein
- EC
- 3.4.22.-
- UniProt
- Q8E0S7
- Ligands
- ETM, SO4, CL
- Pockets
- 8 · best druggability 0.61
Structure
x-ray diffraction · 6 distinct chains · 21% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sortase family protein (EC 3.4.22.-) | protein | 194 | 22% helix, 33% strand | Q8E0S7 |
| B | Sortase family protein (EC 3.4.22.-) | protein | 193 | 18% helix, 31% strand | Q8E0S7 |
| C | Sortase family protein (EC 3.4.22.-) | protein | 189 | 23% helix, 33% strand | Q8E0S7 |
| D | Sortase family protein (EC 3.4.22.-) | protein | 193 | 22% helix, 32% strand | Q8E0S7 |
| E | Sortase family protein (EC 3.4.22.-) | protein | 193 | 21% helix, 32% strand | Q8E0S7 |
| F | Sortase family protein (EC 3.4.22.-) | protein | 188 | 22% helix, 33% strand | Q8E0S7 |
Ligands and binding sites
- ETM · 2-(trimethylammonium)ethyl thiol · ligand · 6 copies · chains A, B, D, C, E, F
- SO4 · Sulfate ion · ion · 5 copies · chains B, C, D, F
- CL · Chloride ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 471 | 0.61 | 0.76 | 74 | SO4 |
| 2 | 422 | 0.58 | 0.75 | 75 | SO4 |
| 3 | 402 | 0.58 | 0.75 | 70 | SO4 |
| 4 | 192 | 0.52 | 0.77 | 25 | ETM |
| 5 | 50 | 0.31 | 0.77 | 14 | empty |
Interfaces
4 interfaces between chains.
- B–D · 428 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 374 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 370 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 361 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 3TBE · The crystal structure of the complex of Streptococcus agalactiae sortase C1 and MTSET · 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 Q8E0S7
- Elsewhere: RCSB PDB 3TBE · PDBe 3TBE · UniProt Q8E0S7
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