MolNFT v1 · #106409 · protein
Crystal structure of carbohydrate transporter solute binding protein VEIS_2079 from verminephrobacter eiseniae EF01-2, target efi-511009, a complex with D-talitol
4RY9 · Periplasmic binding PROTEIN/LACI transcriptional regulator: “Crystal structure of carbohydrate transporter solute binding protein VEIS_2079 from verminephrobacter…”. X-ray diffraction, 2 ligands (TLZ, BCT), 5 pockets (best…
- PDB
- 4RY9
- Type
- protein
- Length
- 594 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Periplasmic binding PROTEIN/LACI transcriptional regulator
- UniProt
- A1WJM2
- Ligands
- TLZ, BCT
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Periplasmic binding PROTEIN/LACI transcriptional regulator | protein | 297 | 45% helix, 20% strand | A1WJM2 |
Ligands and binding sites
- TLZ · D-altritol · ligand · 2 copies · chains A, B
- BCT · Bicarbonate ion · ligand · chains B
- GOL · Glycerol · additive · 14 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 501 | 0.61 | 0.75 | 79 | GOL, BCT |
| 2 | 81 | 0.42 | 0.79 | 18 | GOL |
| 3 | 74 | 0.41 | 0.79 | 18 | GOL |
| 4 | 79 | 0.40 | 0.78 | 14 | empty |
| 5 | 57 | 0.28 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 339 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4RY9 · Crystal structure of carbohydrate transporter solute binding protein VEIS_2079 from… · 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 A1WJM2
- Elsewhere: RCSB PDB 4RY9 · PDBe 4RY9 · UniProt A1WJM2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.