MolNFT v1 · #139877 · protein
Crystal structure of zebrafish lysophosphatidic acid receptor LPA6
5XSZ · Lysophosphatidic acid receptor 6A,ENDOLYSIN…: “Crystal structure of zebrafish lysophosphatidic acid receptor LPA6”. X-ray diffraction, 3 pockets (best druggability 0.72). MolNFT v1 #139877 on GenesisL1: 3D structure, binding sites…
- PDB
- 5XSZ
- Type
- protein
- Length
- 448 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysophosphatidic acid receptor 6A,ENDOLYSIN, lysophosphatidic acid receptor 6A
- EC
- 3.2.1.17
- UniProt
- Q08BG4, P00720
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 73% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysophosphatidic acid receptor 6A,ENDOLYSIN, lysophosphatidic acid receptor 6A (EC 3.2.1.17) | protein | 448 | 73% helix, 3% strand | Q08BG4, P00720 |
Ligands and binding sites
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 3 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.72 | 0.79 | 60 | empty |
| 2 | 556 | 0.67 | 0.76 | 48 | OLC |
| 3 | 159 | 0.41 | 0.74 | 26 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5XSZ · Crystal structure of zebrafish lysophosphatidic acid receptor LPA6 · the same entry in another collection · 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 Q08BG4
- Every structure of UniProt P00720
- Elsewhere: RCSB PDB 5XSZ · PDBe 5XSZ · UniProt Q08BG4 · UniProt P00720
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