MolNFT v1 · #125168 · protein
Crystal structure of N-acylhomoserine lactone dependent luxr family transcriptionl factor CEPR2 from burkholderia cenocepacia
5L10 · N-acylhomoserine lactone dependent regulatory protein: “Crystal structure of N-acylhomoserine lactone dependent luxr family transcriptionl factor CEPR2 from…”. X-ray diffraction, 11 pockets (best druggability 0.79). MolNFT v1…
- PDB
- 5L10
- Type
- protein
- Length
- 1,002 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-acylhomoserine lactone dependent regulatory protein
- UniProt
- B4EHM0
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 50% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-acylhomoserine lactone dependent regulatory protein | protein | 172 | 49% helix, 19% strand | B4EHM0 |
| B | N-acylhomoserine lactone dependent regulatory protein | protein | 170 | 49% helix, 19% strand | B4EHM0 |
| C, D | N-acylhomoserine lactone dependent regulatory protein | protein | 166 | 49% helix, 19% strand | B4EHM0 |
| E | N-acylhomoserine lactone dependent regulatory protein | protein | 164 | 51% helix, 20% strand | B4EHM0 |
| F | N-acylhomoserine lactone dependent regulatory protein | protein | 164 | 51% helix, 20% strand | B4EHM0 |
Ligands and binding sites
- GOL · Glycerol · additive · 7 copies · chains A, E, B, C, D
- FMT · Formic acid · additive · 5 copies · chains A, B, C, D, E
- EDO · 1,2-ethanediol · additive · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 112 | 0.79 | 0.97 | 20 | EDO |
| 2 | 93 | 0.78 | 0.98 | 20 | GOL |
| 3 | 80 | 0.77 | 0.99 | 19 | GOL |
| 4 | 77 | 0.76 | 0.98 | 23 | GOL |
| 5 | 64 | 0.74 | 0.98 | 19 | GOL |
Interfaces
6 interfaces between chains.
- E–F · 1461 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1422 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1360 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 387 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 362 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 5L10 · Crystal Structure of N-Acylhomoserine Lactone Dependent LuxR Family Transcriptionl Factor… · the same entry in another collection · chain A against A, TM-score 1.00
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 B4EHM0
- Elsewhere: RCSB PDB 5L10 · PDBe 5L10 · UniProt B4EHM0
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