Research workbench
Crystal structure of sdgb (udp, nag, and O-glycosylated sd peptide- binding form)
Analyse Crystal structure of sdgb (udp, nag, and O-glycosylated sd peptide- binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VFL
- Type
- protein
- Length
- 1,014 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-ser-asp-ser-asp
- UniProt
- A0A0H2XGN0
- Ligands
- UDP, NAG
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Glycosyl transferase, group 1 family protein | protein | 500 | 33% helix, 27% strand | A0A0H2XGN0 |
| D | Ser-asp-ser-asp-ser-asp-ser-asp | protein | 8 | 63% helix, 0% strand | — |
| G | Ser-asp-ser-asp-ser-asp-ser-asp | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- UDP · Uridine-5'-diphosphate · ligand · 2 copies · chains A, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, C, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 708 | 0.78 | 0.83 | 66 | UDP, NAG |
| 2 | 752 | 0.76 | 0.81 | 66 | UDP, NAG |
| 3 | 862 | 0.75 | 0.78 | 88 | empty |
| 4 | 101 | 0.47 | 0.80 | 20 | empty |
| 5 | 92 | 0.43 | 0.79 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1412 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 308 Ų buried · 13 hydrogen bonds · protein-protein
- C–G · 308 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 glycan (O-glycosylation).
Compared structures
- 7VFL · Crystal structure of SdgB (UDP, NAG, and O-glycosylated SD peptide-binding form) · the same entry in another collection · chain G against G, 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 7VFL · PDBe 7VFL · UniProt A0A0H2XGN0
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