MolNFT v1 · #123046 · protein
Crystal structure of endoglycoceramidase I from rhodococ-cus equi in complex with GM1
5J7Z · Putative secreted endoglycosylceramidase: “Crystal structure of endoglycoceramidase I from rhodococ-cus equi in complex with GM1”. X-ray diffraction, 6 ligands (18C, GAL, BGC), 7 pockets (best druggability 0.82). MolNFT v1 #123046…
- PDB
- 5J7Z
- Type
- protein
- Length
- 886 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative secreted endoglycosylceramidase
- UniProt
- E4W8N9
- Ligands
- 18C, GAL, BGC, NGA, SIA, NA
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative secreted endoglycosylceramidase | protein | 450 | 33% helix, 22% strand | E4W8N9 |
| B | Putative secreted endoglycosylceramidase | protein | 436 | 31% helix, 22% strand | E4W8N9 |
Ligands and binding sites
- 18C · N-((E,2S,3R)-1,3-dihydroxyoctadec-4-en-2-yl)stearamide · ligand · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A
- BGC · beta-D-glucopyranose · sugar · chains A
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · chains A
- SIA · N-acetyl-alpha-neuraminic acid · sugar · chains A
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1135 | 0.82 | 0.83 | 71 | BGC, GAL, 18C |
| 2 | 194 | 0.66 | 0.85 | 29 | empty |
| 3 | 179 | 0.65 | 0.85 | 25 | empty |
| 4 | 146 | 0.57 | 0.82 | 26 | empty |
| 5 | 104 | 0.53 | 0.83 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 838 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5J7Z · Crystal structure of endoglycoceramidase I from Rhodococ-cus equi in complex with GM1 · 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 E4W8N9
- Elsewhere: RCSB PDB 5J7Z · PDBe 5J7Z · UniProt E4W8N9
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