Research workbench
Crystal structure of laci family transcriptional regulator ccpa from weissella paramesenteroides, target efi-512926, with bound sucrose
Analyse Crystal structure of laci family transcriptional regulator ccpa from weissella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RK7
- Type
- protein
- Length
- 540 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucose-resistance amylase regulator
- UniProt
- C5RBT0
- Ligands
- GLC, FRU
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glucose-resistance amylase regulator | protein | 270 | 40% helix, 22% strand | C5RBT0 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- FRU · beta-D-fructofuranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 364 | 0.74 | 0.85 | 40 | GLC, FRU |
| 2 | 362 | 0.73 | 0.85 | 32 | GLC, FRU |
| 3 | 423 | 0.72 | 0.82 | 39 | empty |
| 4 | 96 | 0.46 | 0.80 | 21 | empty |
| 5 | 73 | 0.31 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1470 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 4RK7 · Crystal structure of LacI family transcriptional regulator CCPA from Weissella… · the same entry in another collection · chain B against B, 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 C5RBT0
- Elsewhere: RCSB PDB 4RK7 · PDBe 4RK7 · UniProt C5RBT0
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