MolNFT v1 · #115211 · protein
Crystal structure of endoglycoceramidase I from rhodococ-cus equi
5CCU · Putative secreted endoglycosylceramidase: “Crystal structure of endoglycoceramidase I from rhodococ-cus equi”. X-ray diffraction, 1 ligand (NA), 7 pockets (best druggability 0.83). MolNFT v1 #115211 on GenesisL1: 3D structure…
- PDB
- 5CCU
- Type
- protein
- Length
- 885 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative secreted endoglycosylceramidase
- UniProt
- E4W8N9
- Ligands
- NA
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative secreted endoglycosylceramidase | protein | 449 | 33% helix, 22% strand | E4W8N9 |
| B | Putative secreted endoglycosylceramidase | protein | 436 | 32% helix, 22% strand | E4W8N9 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 894 | 0.83 | 0.84 | 58 | EDO |
| 2 | 193 | 0.64 | 0.84 | 27 | EDO |
| 3 | 168 | 0.59 | 0.83 | 24 | empty |
| 4 | 186 | 0.57 | 0.81 | 32 | EDO |
| 5 | 125 | 0.54 | 0.82 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 941 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5CCU · Crystal structure of endoglycoceramidase I from Rhodococ-cus equi · 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 5CCU · PDBe 5CCU · UniProt E4W8N9
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