Research workbench
Crystal structure of luxp in complex with L-xylulofuranose-1,2-borate
Analyse Crystal structure of luxp in complex with L-xylulofuranose-1,2-borate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YRZ
- Type
- protein
- Length
- 679 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Autoinducer 2-binding periplasmic protein luxp
- UniProt
- P54300
- Ligands
- A2B
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Autoinducer 2-binding periplasmic protein luxp | protein | 339 | 47% helix, 19% strand | P54300 |
| B | Autoinducer 2-binding periplasmic protein luxp | protein | 340 | 46% helix, 19% strand | P54300 |
Ligands and binding sites
- A2B · L-xylulofuranose-1,2-borate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 302 | 0.79 | 0.90 | 47 | A2B |
| 2 | 327 | 0.76 | 0.87 | 44 | A2B |
| 3 | 286 | 0.50 | 0.73 | 43 | empty |
| 4 | 120 | 0.38 | 0.74 | 31 | empty |
| 5 | 68 | 0.36 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 434 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4YRZ · Crystal Structure of LuxP In Complex With L-xylulofuranose-1,2-borate · the same entry in another collection · chain A against A, TM-score 1.00
- P54300 · AlphaFold monomer V2.0 prediction for autoinducer 2-binding periplasmic protein luxp… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P54300
- Elsewhere: RCSB PDB 4YRZ · PDBe 4YRZ · UniProt P54300
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