MolNFT v1 · #98307 · protein
Crystal structures of the lsrr proteins complexed with phospho-ai-2 and its two different analogs reveal distinct mechanisms for ligand recognition
4L5J · Transcriptional regulator lsrr: “Crystal structures of the lsrr proteins complexed with phospho-ai-2 and its two different analogs reveal…”. X-ray diffraction, 1 ligand (HSX), 19 pockets (best druggability 0.62). MolNFT v1 #98307 on…
- PDB
- 4L5J
- Type
- protein
- Length
- 1,232 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator lsrr
- UniProt
- P76141
- Ligands
- HSX
- Pockets
- 19 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Transcriptional regulator lsrr | protein | 308 | 50% helix, 16% strand | P76141 |
Ligands and binding sites
- HSX · 5-O-phosphono-alpha-D-ribofuranose · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.62 | 0.77 | 51 | empty |
| 2 | 150 | 0.62 | 0.85 | 29 | HSX |
| 3 | 289 | 0.61 | 0.79 | 27 | empty |
| 4 | 116 | 0.61 | 0.86 | 30 | HSX |
| 5 | 179 | 0.60 | 0.83 | 36 | HSX |
Interfaces
4 interfaces between chains.
- A–D · 1762 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1676 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 792 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 778 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4L5J · 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 A against A, TM-score 0.80
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 4L5J · PDBe 4L5J · UniProt P76141
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