Research workbench
Protease structure from euphorbia resinifera
Analyse Protease structure from euphorbia resinifera in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EOX
- Type
- protein
- Length
- 1,268 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protease
- Ligands
- NAG, MAN, BMA, XYP, FUC, IOD
- Pockets
- 8 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protease | protein | 634 | 23% helix, 28% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains B, A
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
- XYP · beta-D-xylopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar
- IOD · Iodide ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 720 | 0.67 | 0.76 | 93 | IOD |
| 2 | 216 | 0.66 | 0.84 | 30 | IOD |
| 3 | 194 | 0.66 | 0.85 | 33 | IOD |
| 4 | 433 | 0.61 | 0.76 | 59 | IOD |
| 5 | 207 | 0.47 | 0.74 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 832 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 7EOX · Protease structure from Euphorbia resinifera · 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
- Elsewhere: RCSB PDB 7EOX · PDBe 7EOX
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