Research workbench
The structure of hydra FAM20 with sugar
Analyse The structure of hydra FAM20 with sugar in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XOO
- Type
- protein
- Length
- 700 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycosaminoglycan xylosylkinase
- UniProt
- T2MHS6
- Ligands
- ADN, MBN, NAG, XYP, GAL
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycosaminoglycan xylosylkinase | protein | 349 | 37% helix, 18% strand | T2MHS6 |
| B | Glycosaminoglycan xylosylkinase | protein | 351 | 36% helix, 18% strand | T2MHS6 |
Ligands and binding sites
- ADN · Adenosine · ligand · 2 copies · chains A, B
- MBN · Toluene · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- XYP · beta-D-xylopyranose · sugar · chains A
- GAL · beta-D-galactopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.69 | 0.97 | 19 | empty |
| 2 | 366 | 0.68 | 0.81 | 35 | XYP, ADN |
| 3 | 290 | 0.60 | 0.79 | 38 | ADN |
| 4 | 80 | 0.59 | 0.89 | 22 | empty |
| 5 | 65 | 0.56 | 0.89 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 779 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5XOO · The structure of hydra Fam20 with sugar · 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
- Every structure of UniProt T2MHS6
- Elsewhere: RCSB PDB 5XOO · PDBe 5XOO · UniProt T2MHS6
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