Research workbench
Ternary complex of fixed-arm trx-3OST5 (I299E) with 8MER-1 octasaccharide substrate and co-factor product pap
Analyse Ternary complex of fixed-arm trx-3OST5 (I299E) with 8MER-1 octasaccharide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SCD
- Type
- protein
- Length
- 371 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thioredoxin 1,HEPARAN sulfate glucosamine 3-O- sulfotransferase 5
- EC
- 2.8.2.23
- UniProt
- P0AA25, Q8IZT8
- Ligands
- A3P, BDP, SGN
- Pockets
- 2 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thioredoxin 1,HEPARAN sulfate glucosamine 3-O- sulfotransferase 5 (EC 2.8.2.23) | protein | 371 | 40% helix, 19% strand | P0AA25, Q8IZT8 |
Ligands and binding sites
- A3P · Adenosine-3'-5'-diphosphate · ligand · chains A
- BDP · beta-D-glucopyranuronic acid · sugar · 3 copies · chains A
- SGN · 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose · sugar · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.68 | 0.85 | 36 | A3P |
| 2 | 418 | 0.66 | 0.79 | 51 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7SCD · Ternary complex of fixed-arm Trx-3ost5 (I299E) with 8mer-1 octasaccharide substrate and… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8IZT8 · AlphaFold monomer V2.0 prediction for heparan sulfate glucosamine 3-O-sulfotransferase 5… · a predicted model of the same protein · chain A against A, TM-score 0.71
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 P0AA25
- Every structure of UniProt Q8IZT8
- Elsewhere: RCSB PDB 7SCD · PDBe 7SCD · UniProt P0AA25 · UniProt Q8IZT8
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