Research workbench
Endo-glycoceramidase II from rhodococcus sp.: cellobiose-like imidazole complex
Analyse Endo-glycoceramidase II from rhodococcus sp.: cellobiose-like imidazole complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OYL
- Type
- protein
- Length
- 872 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
- IDC, NA
- Pockets
- 11 · best druggability 0.65
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 | 434 | 32% helix, 21% strand | O33853 |
| B | Endoglycoceramidase II (EC 3.2.1.123) | protein | 438 | 32% helix, 21% strand | O33853 |
Ligands and binding sites
- IDC · (5R,6R,7R,8S)-7,8-dihydroxy-5-(hydroxymethyl)-5,6,7,8-tetrahydroimidazo[1,2-a]pyridin-6-yl beta-D-glucopyranoside · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 4 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 632 | 0.65 | 0.75 | 70 | NA |
| 2 | 148 | 0.64 | 0.86 | 19 | empty |
| 3 | 139 | 0.62 | 0.86 | 20 | empty |
| 4 | 290 | 0.61 | 0.79 | 32 | IDC |
| 5 | 333 | 0.59 | 0.77 | 48 | IDC, GOL |
Interfaces
1 interface between chains.
- A–B · 432 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2OYL · Endo-glycoceramidase II from Rhodococcus sp.: cellobiose-like imidazole 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 2OYL · PDBe 2OYL · UniProt O33853
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