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Crystal structure of heparan sulfate 3-O-sulfotransferase isoform 1 in the presence of pap
Analyse Crystal structure of heparan sulfate 3-O-sulfotransferase isoform 1 in the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VKJ
- Type
- protein
- Length
- 763 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heparan sulfate (glucosamine) 3-O-sulfotransferase 1
- EC
- 2.8.2.23
- UniProt
- O35310
- Ligands
- A3P, SO4
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Heparan sulfate (glucosamine) 3-O-sulfotransferase 1 (EC 2.8.2.23) | protein | 258 | 43% helix, 17% strand | O35310 |
| C | Heparan sulfate (glucosamine) 3-O-sulfotransferase 1 (EC 2.8.2.23) | protein | 247 | 45% helix, 18% strand | O35310 |
Ligands and binding sites
- A3P · Adenosine-3'-5'-diphosphate · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 912 | 0.79 | 0.81 | 76 | A3P |
| 2 | 478 | 0.75 | 0.83 | 65 | SO4, A3P |
| 3 | 284 | 0.67 | 0.82 | 34 | empty |
| 4 | 61 | 0.63 | 0.92 | 18 | empty |
| 5 | 212 | 0.47 | 0.75 | 37 | empty |
Interfaces
3 interfaces between chains.
- A–B · 587 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 332 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 29 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1VKJ · Crystal structure of heparan sulfate 3-O-sulfotransferase isoform 1 in the presence of PAP · the same entry in another collection · chain A against A, TM-score 1.00
- O35310 · AlphaFold monomer V2.0 prediction for heparan sulfate glucosamine 3-O-sulfotransferase 1… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O35310
- Elsewhere: RCSB PDB 1VKJ · PDBe 1VKJ · UniProt O35310
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