MolNFT v1 · #11493 · protein
Crystal structure of autoinducer-2 production protein (luxs) from heamophilus influenzae
1JOE: “Crystal structure of autoinducer-2 production protein (luxs) from heamophilus influenzae”. X-ray diffraction, 2 ligands (HG, ZN), 4 pockets (best druggability 0.61). MolNFT v1 #11493 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1JOE
- Type
- protein
- Length
- 592 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Autoinducer-2 production protein
- UniProt
- P44007
- Ligands
- HG, ZN
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Autoinducer-2 production protein | protein | 148 | 32% helix, 23% strand | P44007 |
Ligands and binding sites
- HG · Mercury (II) ion · metal · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.61 | 0.78 | 30 | ZN |
| 2 | 344 | 0.60 | 0.77 | 29 | ZN |
| 3 | 287 | 0.60 | 0.79 | 27 | ZN |
| 4 | 253 | 0.57 | 0.78 | 25 | ZN |
Interfaces
2 interfaces between chains.
- A–B · 1715 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1708 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 1JOE · Crystal Structure of Autoinducer-2 Production Protein (LuxS) from Heamophilus influenzae · the same entry in another collection · chain A against A, TM-score 1.00
- P44007 · AlphaFold monomer V2.0 prediction for S-ribosylhomocysteine lyase (P44007) · 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 P44007
- Elsewhere: RCSB PDB 1JOE · PDBe 1JOE · UniProt P44007
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