Research workbench
Crystal structure analysis of GM2-activator protein complexed with phosphatidylcholine
Analyse Crystal structure analysis of GM2-activator protein complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AF9
- Type
- protein
- Length
- 163 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ganglioside GM2 activator
- UniProt
- P17900
- Ligands
- DAO, OLA, MYR
- Pockets
- 1 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ganglioside GM2 activator | protein | 163 | 9% helix, 52% strand | P17900 |
Ligands and binding sites
- DAO · Lauric acid · ligand · 2 copies · chains A
- OLA · Oleic acid · ligand · chains A
- MYR · Myristic acid · ligand · chains A
- IPA · Isopropyl alcohol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1074 | 0.76 | 0.78 | 70 | OLA, MYR, DAO, IPA |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2AF9 · Crystal Structure analysis of GM2-Activator protein complexed with phosphatidylcholine · the same entry in another collection · chain A against A, TM-score 1.00
- P17900 · AlphaFold monomer V2.0 prediction for ganglioside GM2 activator (P17900) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P17900
- Elsewhere: RCSB PDB 2AF9 · PDBe 2AF9 · UniProt P17900
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