MolNFT v1 · #189432 · protein
Crystal structure of sdgb (udp and sd peptide-binding form)
7VFM · Glycosyl transferase, group 1 family protein: “Crystal structure of sdgb (udp and sd peptide-binding form)”. X-ray diffraction, 1 ligand (UDP), 8 pockets (best druggability 0.73). MolNFT v1 #189432 on GenesisL1: 3D structure…
- PDB
- 7VFM
- Type
- protein
- Length
- 987 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosyl transferase, group 1 family protein; Ser-asp-ser-asp
- UniProt
- A0A0H2XGN0
- Ligands
- UDP
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosyl transferase, group 1 family protein | protein | 496 | 32% helix, 27% strand | A0A0H2XGN0 |
| C | Glycosyl transferase, group 1 family protein | protein | 485 | 34% helix, 26% strand | A0A0H2XGN0 |
| E | Ser-asp-ser-asp | protein | 4 | 0% helix, 0% strand | — |
| G | Ser-asp-ser-asp | protein | 2 | 0% helix, 0% strand | — |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, C
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 | 701 | 0.73 | 0.79 | 70 | UDP |
| 2 | 661 | 0.73 | 0.79 | 78 | empty |
| 3 | 800 | 0.73 | 0.78 | 81 | UDP |
| 4 | 131 | 0.43 | 0.76 | 26 | empty |
| 5 | 104 | 0.39 | 0.75 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1518 Ų buried · 27 hydrogen bonds · protein-protein
- A–E · 286 Ų buried · 10 hydrogen bonds · protein-protein
- C–G · 121 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7VFM · Crystal structure of SdgB (UDP and SD peptide-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 7VFM · PDBe 7VFM · UniProt A0A0H2XGN0
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