Research workbench
Crystal structure of heparan sulfate 2-O-sulfotransferase from gallus gallus as a maltose binding protein fusion.
Analyse Crystal structure of heparan sulfate 2-O-sulfotransferase from gallus gallus as… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3F5F
- Type
- protein
- Length
- 656 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic protein, heparan sulfate 2-O- sulfotransferase 1
- EC
- 2.8.2.-
- UniProt
- P0AEX9, Q76KB1
- Ligands
- A3P, GLC
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltose-binding periplasmic protein, heparan sulfate 2-O- sulfotransferase 1 (EC 2.8.2.-) | protein | 656 | 46% helix, 17% strand | P0AEX9, Q76KB1 |
Ligands and binding sites
- A3P · Adenosine-3'-5'-diphosphate · ligand · chains A
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
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 | 282 | 0.70 | 0.84 | 30 | GLC |
| 2 | 446 | 0.62 | 0.76 | 50 | A3P |
| 3 | 245 | 0.52 | 0.75 | 41 | empty |
| 4 | 176 | 0.50 | 0.77 | 32 | empty |
| 5 | 108 | 0.46 | 0.79 | 19 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3F5F · Crystal structure of heparan sulfate 2-O-sulfotransferase from gallus gallus as a maltose… · the same entry in another collection · chain A against A, TM-score 1.00
- Q76KB1 · AlphaFold monomer V2.0 prediction for heparan sulfate 2-O-sulfotransferase 1 (Q76KB1) · a predicted model of the same protein · chain A against A, TM-score 0.43
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 P0AEX9
- Every structure of UniProt Q76KB1
- Elsewhere: RCSB PDB 3F5F · PDBe 3F5F · UniProt P0AEX9 · UniProt Q76KB1
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