MolNFT v1 · #22561 · protein
Crystal structure of human 3-O-sulfotransferase-3 with bound pap and tetrasaccharide substrate
1T8U · Heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3A1: “Crystal structure of human 3-O-sulfotransferase-3 with bound pap and tetrasaccharide substrate”. X-ray diffraction, 6 ligands (A3P, UAP, SGN), 3 pockets (best druggability…
- PDB
- 1T8U
- 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
- Ligands
- A3P, UAP, SGN, IDS, NA, SO4
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3A1 | protein | 268 | 43% helix, 15% strand | — |
| B | Heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3A1 | protein | 271 | 44% helix, 15% strand | — |
Ligands and binding sites
- A3P · Adenosine-3'-5'-diphosphate · ligand · 2 copies · chains A, B
- UAP · 4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid · ligand · chains B
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · 2 copies · chains B
- IDS · 2-O-sulfo-alpha-L-idopyranuronic acid · sugar · chains B
- NA · Sodium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains A
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 | 56 | 0.73 | 0.99 | 20 | empty |
| 2 | 232 | 0.69 | 0.85 | 34 | SO4, A3P |
| 3 | 222 | 0.68 | 0.85 | 35 | SGN, A3P |
Interfaces
1 interface between chains.
- A–B · 1864 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 1T8U · Crystal Structure of human 3-O-Sulfotransferase-3 with bound PAP and tetrasaccharide… · 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
- Elsewhere: RCSB PDB 1T8U · PDBe 1T8U
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