Research workbench
Crystal structure of laci family transcriptional regulator from enterococcus faecalis V583, target efi-512923, with bound ribose
Analyse Crystal structure of laci family transcriptional regulator from enterococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RK0
- Type
- protein
- Length
- 1,072 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Laci family sugar-binding transcriptional regulator
- UniProt
- Q82ZT5
- Ligands
- RIB
- Pockets
- 13 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Laci family sugar-binding transcriptional regulator | protein | 268 | 41% helix, 21% strand | Q82ZT5 |
| B | Laci family sugar-binding transcriptional regulator | protein | 267 | 40% helix, 20% strand | Q82ZT5 |
| D | Laci family sugar-binding transcriptional regulator | protein | 269 | 39% helix, 22% strand | Q82ZT5 |
Ligands and binding sites
- RIB · 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
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 635 | 0.72 | 0.79 | 89 | RIB |
| 2 | 481 | 0.70 | 0.80 | 62 | empty |
| 3 | 283 | 0.56 | 0.77 | 44 | RIB |
| 4 | 260 | 0.55 | 0.77 | 41 | RIB |
| 5 | 65 | 0.45 | 0.83 | 21 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1856 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1852 Ų buried · 27 hydrogen bonds · protein-protein
- A–D · 548 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 4RK0 · Crystal structure of LacI family transcriptional regulator from Enterococcus faecalis… · 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 Q82ZT5
- Elsewhere: RCSB PDB 4RK0 · PDBe 4RK0 · UniProt Q82ZT5
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