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Crystal structure of heparan sulfate 6-O-sulfotransferase with bound pap and glucuronic acid containing hexasaccharide substrate
Analyse Crystal structure of heparan sulfate 6-O-sulfotransferase with bound pap and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T03
- Type
- protein
- Length
- 1,345 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose binding protein - heparan sulfate 6-O- sulfotransferase isoform 3 fusion protein
- EC
- 2.8.2.-
- UniProt
- P0AEY0, A0MGZ7
- Ligands
- GNS, A3P, NPO, GLC, BDP, NA, CL
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltose binding protein - heparan sulfate 6-O- sulfotransferase isoform 3 fusion protein (EC 2.8.2.-) | protein | 670 | 44% helix, 16% strand | P0AEY0, A0MGZ7 |
| B | Maltose binding protein - heparan sulfate 6-O- sulfotransferase isoform 3 fusion protein (EC 2.8.2.-) | protein | 675 | 46% helix, 16% strand | P0AEY0, A0MGZ7 |
Ligands and binding sites
- GNS · 2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose · ligand · 6 copies · chains A, B
- A3P · Adenosine-3'-5'-diphosphate · ligand · 2 copies · chains A, B
- NPO · P-nitrophenol · ligand · 2 copies
- GLC · alpha-D-glucopyranose · sugar · 8 copies · chains A, B
- BDP · beta-D-glucopyranuronic acid · sugar · 6 copies · chains A, B
- NA · Sodium ion · metal · 6 copies · chains A, B
- CL · Chloride ion · ion · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 16 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 754 | 0.75 | 0.80 | 50 | GLC |
| 2 | 353 | 0.72 | 0.83 | 34 | GLC |
| 3 | 756 | 0.70 | 0.77 | 58 | EDO |
| 4 | 743 | 0.69 | 0.76 | 69 | GNS, A3P, EDO |
| 5 | 184 | 0.68 | 0.87 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 815 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 5T03 · Crystal structure of heparan sulfate 6-O-sulfotransferase with bound PAP and glucuronic… · the same entry in another collection · chain A against A, TM-score 1.00
- A0MGZ7 · AlphaFold monomer V2.0 prediction for heparan-sulfate 6-O-sulfotransferase 3-B (A0MGZ7) · a predicted model of the same protein · chain B against A, TM-score 0.45
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 P0AEY0
- Every structure of UniProt A0MGZ7
- Elsewhere: RCSB PDB 5T03 · PDBe 5T03 · UniProt P0AEY0 · UniProt A0MGZ7
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