MolNFT v1 · #9439 · protein
EBULIN,ORTHORHOMBIC crystal form model
1HWM: “EBULIN,ORTHORHOMBIC crystal form model”. X-ray diffraction, 4 ligands (NAG, BMA, MAN), 4 pockets (best druggability 0.65). MolNFT v1 #9439 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1HWM
- Type
- protein
- Length
- 515 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, BMA, MAN, GAL
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ebulin (EC 3.2.2.22) | protein | 251 | 40% helix, 24% strand | Q9AVR2 |
| B | Ebulin (EC 3.2.2.22) | protein | 264 | 8% helix, 40% strand | Q9AVR2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar
- GAL · beta-D-galactopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 264 | 0.65 | 0.82 | 34 | empty |
| 2 | 167 | 0.60 | 0.83 | 23 | empty |
| 3 | 164 | 0.50 | 0.78 | 27 | empty |
| 4 | 158 | 0.47 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1697 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 1HWM · EBULIN,ORTHORHOMBIC crystal form model · 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 1HWM · PDBe 1HWM · UniProt Q9AVR2
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