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Structure of human sphingomyelinase phosphodiesterase like 3A (SMPDL3A) with ZN2+
Analyse Structure of human sphingomyelinase phosphodiesterase like 3A (SMPDL3A) with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EBB
- Type
- protein
- Length
- 1,230 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acid sphingomyelinase-like phosphodiesterase 3A
- EC
- 3.1.4.-
- UniProt
- Q92484
- Ligands
- NAG, ZN
- Pockets
- 14 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Acid sphingomyelinase-like phosphodiesterase 3A (EC 3.1.4.-) | protein | 410 | 36% helix, 20% strand | Q92484 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B, C
- ZN · Zinc ion · metal · 6 copies · chains A, B, C
- MLI · Malonate ion · additive · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 743 | 0.67 | 0.75 | 65 | GOL |
| 2 | 260 | 0.65 | 0.83 | 42 | empty |
| 3 | 255 | 0.65 | 0.83 | 40 | empty |
| 4 | 268 | 0.52 | 0.75 | 36 | MLI |
| 5 | 265 | 0.51 | 0.75 | 32 | MLI |
Interfaces
3 interfaces between chains.
- A–C · 487 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 476 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 237 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 9 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
- 5EBB · Structure of human sphingomyelinase phosphodiesterase like 3A (SMPDL3A) with Zn2+ · the same entry in another collection · chain A against A, TM-score 1.00
- Q92484 · AlphaFold monomer V2.0 prediction for acid sphingomyelinase-like phosphodiesterase 3A… · a predicted model of the same protein · 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 Q92484
- Elsewhere: RCSB PDB 5EBB · PDBe 5EBB · UniProt Q92484
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