MolNFT v1 · #111383 · protein
Crystal structure of luxp in complex with a formose derived ai-2 analogue
4YP9 · Autoinducer 2-binding periplasmic protein luxp: “Crystal structure of luxp in complex with a formose derived ai-2 analogue”. X-ray diffraction, 3 ligands (A1B, MG, CA), 7 pockets (best druggability 0.85). MolNFT v1 #111383 on…
- PDB
- 4YP9
- 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
- A1B, MG, CA
- Pockets
- 7 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Autoinducer 2-binding periplasmic protein luxp | protein | 337 | 44% helix, 19% strand | P54300 |
| B | Autoinducer 2-binding periplasmic protein luxp | protein | 342 | 46% helix, 18% strand | P54300 |
Ligands and binding sites
- A1B · 1-deoxy-alpha-L-xylulofuranose-1,2-borate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1115 | 0.85 | 0.86 | 117 | A1B |
| 2 | 313 | 0.74 | 0.86 | 39 | A1B |
| 3 | 120 | 0.47 | 0.78 | 22 | empty |
| 4 | 116 | 0.46 | 0.78 | 16 | empty |
| 5 | 113 | 0.43 | 0.77 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 929 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4YP9 · Crystal Structure of LuxP In Complex With a Formose Derived AI-2 Analogue · 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 0.98
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 4YP9 · PDBe 4YP9 · UniProt P54300
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