Research workbench
Crystal structure of the autoinducer-2-bound form of vibrio harveyi luxp complexed with the periplasmic domain of luxq
Analyse Crystal structure of the autoinducer-2-bound form of vibrio harveyi luxp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HJ9
- Type
- protein
- Length
- 1,081 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Autoinducer 2-binding periplasmic protein luxp; Autoinducer 2 sensor KINASE/PHOSPHATASE…
- EC
- 3.1.3.-
- UniProt
- P54300, P54302
- Ligands
- AI2
- Pockets
- 16 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Autoinducer 2-binding periplasmic protein luxp | protein | 339 | 46% helix, 18% strand | P54300 |
| B | Autoinducer 2-binding periplasmic protein luxp | protein | 329 | 46% helix, 19% strand | P54300 |
| C | Autoinducer 2 sensor KINASE/PHOSPHATASE luxq (EC 3.1.3.-) | protein | 210 | 39% helix, 33% strand | P54302 |
| D | Autoinducer 2 sensor KINASE/PHOSPHATASE luxq (EC 3.1.3.-) | protein | 203 | 34% helix, 35% strand | P54302 |
Ligands and binding sites
- AI2 · 3A-methyl-5,6-dihydro-furo[2,3-d][1,3,2]dioxaborole-2,2,6,6A-tetraol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1181 | 0.80 | 0.81 | 102 | empty |
| 2 | 111 | 0.77 | 0.97 | 31 | AI2 |
| 3 | 191 | 0.67 | 0.86 | 25 | empty |
| 4 | 674 | 0.66 | 0.75 | 53 | empty |
| 5 | 218 | 0.63 | 0.82 | 35 | AI2 |
Interfaces
4 interfaces between chains.
- A–C · 1366 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 897 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 760 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 715 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2HJ9 · Crystal structure of the Autoinducer-2-bound form of Vibrio harveyi LuxP complexed with… · the same entry in another collection · chain D against D, 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 0.99
- P54302 · AlphaFold monomer V2.0 prediction for autoinducer 2 sensor KINASE/PHOSPHATASE luxq… · a predicted model of the same protein · chain D 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
- Every structure of UniProt P54302
- Elsewhere: RCSB PDB 2HJ9 · PDBe 2HJ9 · UniProt P54300 · UniProt P54302
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