Research workbench
Crystal structures of the lsrr proteins complexed with phospho-ai-2 and its two different analogs reveal distinct mechanisms for ligand recognition
Analyse Crystal structures of the lsrr proteins complexed with phospho-ai-2 and its two… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4L50
- Type
- protein
- Length
- 495 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator lsrr
- UniProt
- P76141
- Ligands
- D8X
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulator lsrr | protein | 248 | 49% helix, 16% strand | P76141 |
| B | Transcriptional regulator lsrr | protein | 247 | 47% helix, 17% strand | P76141 |
Ligands and binding sites
- D8X · (2S)-2,3,3-trihydroxy-6-methyl-4-oxoheptyl dihydrogen phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 193 | 0.69 | 0.87 | 42 | D8X |
| 2 | 173 | 0.68 | 0.87 | 37 | D8X |
| 3 | 142 | 0.41 | 0.74 | 31 | empty |
| 4 | 164 | 0.40 | 0.72 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 830 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4L50 · Crystal structures of the LsrR proteins complexed with phospho-AI-2 and its two different… · the same entry in another collection · chain A against A, TM-score 1.00
- P76141 · AlphaFold monomer V2.0 prediction for transcriptional regulator lsrr (P76141) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P76141
- Elsewhere: RCSB PDB 4L50 · PDBe 4L50 · UniProt P76141
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