Research workbench
Crystal structure of sphingomyelinase from bacillus cereus with calcium ion
Analyse Crystal structure of sphingomyelinase from bacillus cereus with calcium ion in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DDR
- Type
- protein
- Length
- 1,173 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sphingomyelin phosphodiesterase
- EC
- 3.1.4.12
- UniProt
- P11889
- Ligands
- CA
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sphingomyelin phosphodiesterase (EC 3.1.4.12) | protein | 288 | 19% helix, 33% strand | P11889 |
| B | Sphingomyelin phosphodiesterase (EC 3.1.4.12) | protein | 289 | 19% helix, 33% strand | P11889 |
| C, D | Sphingomyelin phosphodiesterase (EC 3.1.4.12) | protein | 298 | 19% helix, 32% strand | P11889 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1109 | 0.81 | 0.82 | 100 | empty |
| 2 | 656 | 0.70 | 0.78 | 54 | empty |
| 3 | 434 | 0.62 | 0.76 | 42 | CA |
| 4 | 426 | 0.61 | 0.76 | 43 | CA |
| 5 | 315 | 0.54 | 0.75 | 43 | CA |
Interfaces
4 interfaces between chains.
- A–D · 435 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 413 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 393 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 205 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2DDR · Crystal structure of sphingomyelinase from Bacillus cereus with calcium ion · the same entry in another collection · chain A against A, TM-score 1.00
- P11889 · AlphaFold monomer V2.0 prediction for sphingomyelinase C (P11889) · 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 P11889
- Elsewhere: RCSB PDB 2DDR · PDBe 2DDR · UniProt P11889
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.