Research workbench
Crystal structure of human 3-O-sulfotransferase-3 with bound pap
Analyse Crystal structure of human 3-O-sulfotransferase-3 with bound pap in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1T8T
- Type
- protein
- Length
- 539 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3A1
- UniProt
- Q9Y662
- Ligands
- A3P
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3A1 | protein | 268 | 45% helix, 15% strand | Q9Y662 |
| B | Heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3A1 | protein | 271 | 44% helix, 15% strand | Q9Y662 |
Ligands and binding sites
- A3P · Adenosine-3'-5'-diphosphate · ligand · 2 copies · chains A, B
- CIT · Citric acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.72 | 0.98 | 20 | empty |
| 2 | 223 | 0.69 | 0.86 | 34 | A3P |
| 3 | 246 | 0.67 | 0.84 | 37 | A3P |
Interfaces
1 interface between chains.
- A–B · 1832 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1T8T · Crystal Structure of human 3-O-Sulfotransferase-3 with bound PAP · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y662 · AlphaFold monomer V2.0 prediction for heparan sulfate glucosamine 3-O-sulfotransferase… · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q9Y662
- Elsewhere: RCSB PDB 1T8T · PDBe 1T8T · UniProt Q9Y662
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