Research workbench
Crystal Structure of the Alpha-ribazole Phosphatase from Shigella flexneri
Analyse Crystal Structure of the Alpha-ribazole Phosphatase from Shigella flexneri in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NRU
- Type
- protein
- Length
- 2,425 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.505
- Source
- Shigella flexneri 2a
- Molecule
- CobC
- EC
- 3.1.3.73
- UniProt
- A0A2Y2SF70
- Ligands
- SO4, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · resolution 2.505 · 3 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, J | CobC (EC 3.1.3.73) | protein | 202 | 42% helix, 20% strand | A0A2Y2SF70 |
| I, K | CobC (EC 3.1.3.73) | protein | 203 | 42% helix, 20% strand | A0A2Y2SF70 |
| L | CobC (EC 3.1.3.73) | protein | 201 | 42% helix, 21% strand | A0A2Y2SF70 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- CL · Chloride ion · ion · 6 copies · chains D, F, I, J, K, L
- PEG · Di(hydroxyethyl)ether · additive · 9 copies · chains A, E, F, G, H, L
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, F, H, I, J
- GOL · Glycerol · additive · 4 copies · chains C, G, I
- PG4 · Tetraethylene glycol · additive · 2 copies · chains A, B, C, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1007 | 0.86 | 0.87 | 99 | SO4, GOL |
| 2 | 1084 | 0.86 | 0.87 | 102 | SO4 |
| 3 | 251 | 0.58 | 0.78 | 23 | SO4, GOL |
| 4 | 243 | 0.58 | 0.78 | 25 | SO4, PG4, PEG |
| 5 | 252 | 0.58 | 0.78 | 24 | SO4, PEG |
Interfaces
14 interfaces between chains.
- D–E · 893 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 882 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 868 Ų buried · 17 hydrogen bonds · protein-protein
- I–L · 867 Ų buried · 17 hydrogen bonds · protein-protein
- C–J · 834 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 72 modified (engineered).
Compared structures
- 6NRU · Crystal structure of the alpha-ribazole phosphatase from shigella flexneri · 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 A0A2Y2SF70
- Elsewhere: RCSB PDB 6NRU · PDBe 6NRU · UniProt A0A2Y2SF70
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