MolNFT v1 · #105931 · protein
Crystal structure of laci family transcriptional regulator from enterococcus faecium, target efi-512930, with bound ribose
4RK1 · Ribose transcriptional regulator: “Crystal structure of laci family transcriptional regulator from enterococcus faecium, target efi-512930, with…”. X-ray diffraction, 2 ligands (RIB, CL), 15 pockets (best druggability 0.72). MolNFT…
- PDB
- 4RK1
- Type
- protein
- Length
- 1,608 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribose transcriptional regulator
- UniProt
- I3TZ89
- Ligands
- RIB, CL
- Pockets
- 15 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribose transcriptional regulator | protein | 267 | 40% helix, 21% strand | I3TZ89 |
| B, C, E, F | Ribose transcriptional regulator | protein | 268 | 42% helix, 22% strand | I3TZ89 |
| D | Ribose transcriptional regulator | protein | 269 | 41% helix, 22% strand | I3TZ89 |
Ligands and binding sites
- RIB · alpha-D-ribofuranose · ligand · 6 copies · chains A, B, C, D, E, F
- CL · Chloride ion · ion · 21 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 684 | 0.72 | 0.79 | 107 | RIB, CL |
| 2 | 484 | 0.69 | 0.80 | 85 | RIB, CL |
| 3 | 418 | 0.68 | 0.80 | 71 | RIB, CL |
| 4 | 247 | 0.61 | 0.80 | 24 | empty |
| 5 | 258 | 0.61 | 0.80 | 26 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1856 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1824 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1659 Ų buried · 19 hydrogen bonds · protein-protein
- B–F · 454 Ų buried · 3 hydrogen bonds · protein-protein
- C–F · 432 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 4RK1 · Crystal structure of LacI family transcriptional regulator from Enterococcus faecium… · 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 I3TZ89
- Elsewhere: RCSB PDB 4RK1 · PDBe 4RK1 · UniProt I3TZ89
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