MolNFT v1 · #189430 · protein
Crystal structure of sdgb (ligand-free form)
7VFK · Glycosyl transferase, group 1 family protein: “Crystal structure of sdgb (ligand-free form)”. X-ray diffraction, 9 pockets (best druggability 0.73). MolNFT v1 #189430 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7VFK
- Type
- protein
- Length
- 991 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl transferase, group 1 family protein
- UniProt
- A0A0H2XGN0
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyl transferase, group 1 family protein | protein | 499 | 33% helix, 27% strand | A0A0H2XGN0 |
| B | Glycosyl transferase, group 1 family protein | protein | 492 | 34% helix, 27% strand | A0A0H2XGN0 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 638 | 0.73 | 0.79 | 70 | GOL, PGE |
| 2 | 661 | 0.72 | 0.79 | 73 | empty |
| 3 | 739 | 0.71 | 0.77 | 80 | GOL |
| 4 | 183 | 0.54 | 0.79 | 33 | empty |
| 5 | 136 | 0.46 | 0.77 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1446 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 7VFK · Crystal structure of SdgB (ligand-free form) · 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 A0A0H2XGN0
- Elsewhere: RCSB PDB 7VFK · PDBe 7VFK · UniProt A0A0H2XGN0
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