MolNFT v1 · #30990 · protein
Crystal structure analysis of GM2-activator protein complexed with phosphatidylcholine
2AG4 · Ganglioside GM2 activator: “Crystal structure analysis of GM2-activator protein complexed with phosphatidylcholine”. X-ray diffraction, 2 ligands (LP3, OLA), 4 pockets (best druggability 0.76). MolNFT v1 #30990 on GenesisL1: 3D…
- PDB
- 2AG4
- Type
- protein
- Length
- 328 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ganglioside GM2 activator
- UniProt
- P17900
- Ligands
- LP3, OLA
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ganglioside GM2 activator | protein | 164 | 7% helix, 52% strand | P17900 |
Ligands and binding sites
- LP3 · (7R)-4,7-dihydroxy-N,N,N-trimethyl-10-oxo-3,5,9-trioxa-4-phosphaheptacosan-1-aminium 4-oxide · ligand · 2 copies · chains A, B
- OLA · Oleic acid · ligand · 2 copies · chains A, B
- IPA · Isopropyl alcohol · additive · 12 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1193 | 0.76 | 0.78 | 67 | LP3, IPA |
| 2 | 1178 | 0.76 | 0.78 | 60 | LP3, IPA |
| 3 | 169 | 0.46 | 0.75 | 18 | empty |
| 4 | 60 | 0.30 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 264 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2AG4 · 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 0.92
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 2AG4 · PDBe 2AG4 · UniProt P17900
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.