Research workbench
Ebulin complexed with galactose, trigonal crystal form
Analyse Ebulin complexed with galactose, trigonal crystal form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HWN
- Type
- protein
- Length
- 517 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ebulin
- EC
- 3.2.2.22
- UniProt
- Q9AVR2
- Ligands
- NAG, GAL
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ebulin (EC 3.2.2.22) | protein | 254 | 37% helix, 22% strand | Q9AVR2 |
| B | Ebulin (EC 3.2.2.22) | protein | 263 | 7% helix, 32% strand | Q9AVR2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 251 | 0.72 | 0.87 | 28 | empty |
| 2 | 51 | 0.68 | 0.97 | 23 | empty |
| 3 | 244 | 0.61 | 0.81 | 36 | empty |
| 4 | 204 | 0.55 | 0.79 | 31 | empty |
| 5 | 134 | 0.49 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1733 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 1HWN · Ebulin complexed with galactose, trigonal crystal form · 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 Q9AVR2
- Elsewhere: RCSB PDB 1HWN · PDBe 1HWN · UniProt Q9AVR2
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