Research workbench
Endo-glycoceramidase II from rhodococcus sp.: ganglioside GM3 complex
Analyse Endo-glycoceramidase II from rhodococcus sp.: ganglioside GM3 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OSX
- Type
- protein
- Length
- 449 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoglycoceramidase II
- EC
- 3.2.1.123
- UniProt
- O33853
- Ligands
- 16C, BGC, GAL, SIA, NA
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoglycoceramidase II (EC 3.2.1.123) | protein | 449 | 33% helix, 21% strand | O33853 |
Ligands and binding sites
- 16C · N-((E,2S,3R)-1,3-dihydroxyoctadec-4-en-2-yl)palmitamide · ligand · chains A
- BGC · beta-D-glucopyranose · sugar · chains A
- GAL · beta-D-galactopyranose · sugar · chains A
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains A
- NA · Sodium ion · metal · 4 copies · chains A
- GOL · Glycerol · additive · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.66 | 0.79 | 46 | BGC, GAL, 16C |
| 2 | 149 | 0.62 | 0.85 | 22 | empty |
| 3 | 85 | 0.37 | 0.77 | 18 | NA |
| 4 | 71 | 0.35 | 0.77 | 14 | empty |
| 5 | 56 | 0.31 | 0.76 | 15 | empty |
Compared structures
- 2OSX · Endo-glycoceramidase II from Rhodococcus sp.: Ganglioside GM3 Complex · 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 O33853
- Elsewhere: RCSB PDB 2OSX · PDBe 2OSX · UniProt O33853
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