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Structure of the AI-2 processing enzyme LsrF in complex with the product of the LsrG reaction P-HPD
Analyse Structure of the AI-2 processing enzyme LsrF in complex with the product of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4P2V
- Type
- protein
- Length
- 2,809 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.51
- Source
- Escherichia coli
- Molecule
- Uncharacterized aldolase LsrF
- EC
- 4.1.2.-
- UniProt
- P76143
- Ligands
- 26T
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · resolution 2.51 · 2 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, G, H, I, K | Uncharacterized aldolase LsrF (EC 4.1.2.-) | protein | 281 | 39% helix, 15% strand | P76143 |
| F | Uncharacterized aldolase LsrF (EC 4.1.2.-) | protein | 280 | 41% helix, 14% strand | P76143 |
Ligands and binding sites
- 26T · (3R)-3-hydroxy-2,4-dioxopentyl dihydrogen phosphate · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, K
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 255 | 0.70 | 0.86 | 29 | 26T |
| 2 | 396 | 0.70 | 0.81 | 44 | 26T |
| 3 | 215 | 0.70 | 0.86 | 27 | 26T |
| 4 | 238 | 0.68 | 0.85 | 31 | 26T |
| 5 | 189 | 0.68 | 0.87 | 25 | 26T |
Interfaces
25 interfaces between chains.
- B–I · 2144 Ų buried · 32 hydrogen bonds · protein-protein
- E–F · 2134 Ų buried · 37 hydrogen bonds · protein-protein
- D–G · 2119 Ų buried · 34 hydrogen bonds · protein-protein
- A–K · 2080 Ų buried · 40 hydrogen bonds · protein-protein
- C–H · 2075 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 4P2V · Structure of the ai-2 processing enzyme lsrf in complex with the product of the lsrg… · the same entry in another collection · chain K against K, TM-score 1.00
- P76143 · AlphaFold monomer V2.0 prediction for 3-hydroxy-5-phosphonooxypentane-2,4-dione thiolase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P76143
- Elsewhere: RCSB PDB 4P2V · PDBe 4P2V · UniProt P76143
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