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Structure of human sphingomyelinase phosphodiesterase like 3A (SMPDL3A) with 5' cmp
Analyse Structure of human sphingomyelinase phosphodiesterase like 3A (SMPDL3A) with 5'… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5EBE
- Type
- protein
- Length
- 1,248 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
- C5P, RP5, NAG, ZN, SCN
- Pockets
- 13 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acid sphingomyelinase-like phosphodiesterase 3A (EC 3.1.4.-) | protein | 418 | 36% helix, 20% strand | Q92484 |
| B, C | Acid sphingomyelinase-like phosphodiesterase 3A (EC 3.1.4.-) | protein | 415 | 34% helix, 20% strand | Q92484 |
Ligands and binding sites
- C5P · Cytidine-5'-monophosphate · ligand · 2 copies · chains A, C
- RP5 · 5-O-phosphono-beta-D-ribofuranose · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains B, A, C
- ZN · Zinc ion · metal · 6 copies · chains A, B, C
- SCN · Thiocyanate ion · ion · 2 copies · chains C
- GOL · Glycerol · additive · 2 copies · chains B
- MLI · Malonate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 908 | 0.68 | 0.74 | 72 | empty |
| 2 | 317 | 0.67 | 0.82 | 44 | empty |
| 3 | 351 | 0.66 | 0.81 | 49 | empty |
| 4 | 274 | 0.52 | 0.75 | 34 | C5P |
| 5 | 251 | 0.51 | 0.75 | 34 | ZN, C5P |
Interfaces
3 interfaces between chains.
- A–B · 497 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 488 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 149 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 glycan, 6 disulfide (N-glycosylation, disulfide).
Compared structures
- 5EBE · Structure of human sphingomyelinase phosphodiesterase like 3A (SMPDL3A) with 5' CMP · 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 C 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 5EBE · PDBe 5EBE · UniProt Q92484
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