MolNFT v1 · #47248 · protein
Endo-glycoceramidase II from rhodococcus sp.
2OSW · Endoglycoceramidase II: “Endo-glycoceramidase II from rhodococcus sp.”. X-ray diffraction, 1 ligand (NA), 13 pockets (best druggability 0.63). MolNFT v1 #47248 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2OSW
- Type
- protein
- Length
- 871 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoglycoceramidase II
- EC
- 3.2.1.123
- UniProt
- O33853
- Ligands
- NA
- Pockets
- 13 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoglycoceramidase II (EC 3.2.1.123) | protein | 433 | 32% helix, 21% strand | O33853 |
| B | Endoglycoceramidase II (EC 3.2.1.123) | protein | 438 | 33% helix, 21% strand | O33853 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.63 | 0.85 | 19 | empty |
| 2 | 149 | 0.62 | 0.85 | 21 | empty |
| 3 | 292 | 0.60 | 0.78 | 39 | TRS |
| 4 | 496 | 0.60 | 0.74 | 45 | empty |
| 5 | 307 | 0.58 | 0.77 | 39 | TRS |
Interfaces
1 interface between chains.
- A–B · 439 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2OSW · Endo-glycoceramidase II from Rhodococcus sp. · 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 2OSW · PDBe 2OSW · UniProt O33853
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