Research workbench
Crystal structure of human acid ceramidase in covalent complex with carmofur
Analyse Crystal structure of human acid ceramidase in covalent complex with carmofur in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MHM
- Type
- protein
- Length
- 734 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acid ceramidase subunit alpha; Acid ceramidase subunit beta
- EC
- 3.5.1.23
- UniProt
- Q13510
- Ligands
- JRY, NAG, SO4
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Acid ceramidase subunit alpha (EC 3.5.1.23) | protein | 114 | 59% helix, 8% strand | Q13510 |
| B, D | Acid ceramidase subunit beta (EC 3.5.1.23) | protein | 253 | 24% helix, 34% strand | Q13510 |
Ligands and binding sites
- JRY · hexylcarbamic acid · ligand · 2 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 13 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 436 | 0.76 | 0.84 | 57 | JRY |
| 2 | 478 | 0.76 | 0.83 | 54 | JRY |
| 3 | 635 | 0.64 | 0.75 | 59 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2987 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 2983 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 235 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 7 glycan, 4 disulfide, 2 covalent (N-glycosylation, disulfide, covalent ligand).
Compared structures
- 6MHM · Crystal structure of human acid ceramidase in covalent complex with carmofur · the same entry in another collection · chain C against C, TM-score 1.00
- Q13510 · AlphaFold monomer V2.0 prediction for acid ceramidase (Q13510) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 Q13510
- Elsewhere: RCSB PDB 6MHM · PDBe 6MHM · UniProt Q13510
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