MolNFT v1 · #189434 · protein
Crystal structure of sdgb (phosphate-binding form)
7VFO · Glycosyl transferase, group 1 family protein: “Crystal structure of sdgb (phosphate-binding form)”. X-ray diffraction, 1 ligand (PO4), 8 pockets (best druggability 0.78). MolNFT v1 #189434 on GenesisL1: 3D structure, binding sites…
- PDB
- 7VFO
- Type
- protein
- Length
- 990 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl transferase, group 1 family protein
- UniProt
- A0A0H2XGN0
- Ligands
- PO4
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyl transferase, group 1 family protein | protein | 496 | 31% helix, 27% strand | A0A0H2XGN0 |
| B | Glycosyl transferase, group 1 family protein | protein | 494 | 31% helix, 26% strand | A0A0H2XGN0 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 11 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 727 | 0.78 | 0.82 | 78 | PO4 |
| 2 | 662 | 0.77 | 0.82 | 77 | PO4 |
| 3 | 679 | 0.64 | 0.74 | 60 | empty |
| 4 | 81 | 0.43 | 0.80 | 14 | empty |
| 5 | 109 | 0.41 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 164 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 modified (engineered).
Compared structures
- 7VFO · Crystal structure of SdgB (Phosphate-binding 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 7VFO · PDBe 7VFO · UniProt A0A0H2XGN0
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