Research workbench
Crystal structure of human alkaline ceramidase 3 (ACER3) at 2.7 ångström resolution
Analyse Crystal structure of human alkaline ceramidase 3 (ACER3) at 2.7 ångström… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6G7O
- Type
- protein
- Length
- 350 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkaline ceramidase 3,SOLUBLE cytochrome B562
- EC
- 3.5.1.-
- UniProt
- Q9NUN7, P0ABE7
- Ligands
- OLB, NA, MG, ZN, CA, SO4
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alkaline ceramidase 3,SOLUBLE cytochrome B562 (EC 3.5.1.-) | protein | 350 | 75% helix, 0% strand | Q9NUN7, P0ABE7 |
Ligands and binding sites
- OLB · (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · ligand · chains A
- NA · Sodium ion · metal · 3 copies · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- ZN · Zinc ion · metal · chains A
- CA · Calcium ion · metal · chains A
- SO4 · Sulfate ion · ion · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 257 | 0.79 | 0.91 | 42 | ZN, OLB |
| 2 | 73 | 0.33 | 0.75 | 12 | empty |
| 3 | 54 | 0.30 | 0.76 | 15 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6G7O · Crystal structure of human alkaline ceramidase 3 (ACER3) at 2.7 Angstrom resolution · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NUN7 · AlphaFold monomer V2.0 prediction for alkaline ceramidase 3 (Q9NUN7) · a predicted model of the same protein · chain A against A, TM-score 0.69
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain A against A, TM-score 0.30
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 Q9NUN7
- Every structure of UniProt P0ABE7
- Elsewhere: RCSB PDB 6G7O · PDBe 6G7O · UniProt Q9NUN7 · UniProt P0ABE7
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