Research workbench
Crystal structure of the apo form of vibrio harveyi luxp complexed with the periplasmic domain of luxq
Analyse Crystal structure of the apo form of vibrio harveyi luxp complexed with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZHH
- Type
- protein
- Length
- 552 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Autoinducer 2-binding periplasmic protein luxp; Autoinducer 2 sensor KINASE/PHOSPHATASE…
- UniProt
- P54300, P54302
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Autoinducer 2-binding periplasmic protein luxp | protein | 344 | 46% helix, 19% strand | P54300 |
| B | Autoinducer 2 sensor KINASE/PHOSPHATASE luxq | protein | 208 | 38% helix, 33% strand | P54302 |
Ligands and binding sites
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · chains A, 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 309 | 0.64 | 0.81 | 36 | empty |
| 2 | 309 | 0.61 | 0.79 | 30 | NHE |
| 3 | 439 | 0.60 | 0.75 | 53 | empty |
| 4 | 54 | 0.38 | 0.80 | 10 | empty |
| 5 | 67 | 0.32 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1169 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 1ZHH · Crystal Structure of the Apo Form of Vibrio Harveyi LUXP Complexed with the Periplasmic… · the same entry in another collection · chain A against A, TM-score 1.00
- P54302 · AlphaFold monomer V2.0 prediction for autoinducer 2 sensor KINASE/PHOSPHATASE luxq… · a predicted model of the same protein · chain B against A, TM-score 0.98
- 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 0.84
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
- Every structure of UniProt P54302
- Elsewhere: RCSB PDB 1ZHH · PDBe 1ZHH · UniProt P54300 · UniProt P54302
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