Research workbench
Crystal structure of a lipid G protein-coupled receptor at 3.35A
Analyse Crystal structure of a lipid G protein-coupled receptor at 3.35A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3V2W
- Type
- protein
- Length
- 442 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sphingosine 1-phosphate receptor 1, lysozyme chimera
- EC
- 3.2.1.17
- UniProt
- P21453, P00720
- Ligands
- ML5, NAG
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 70% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sphingosine 1-phosphate receptor 1, lysozyme chimera (EC 3.2.1.17) | protein | 442 | 70% helix, 3% strand | P21453, P00720 |
Ligands and binding sites
- ML5 · {(3R)-3-amino-4-[(3-hexylphenyl)amino]-4-oxobutyl}phosphonic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 336 | 0.75 | 0.86 | 44 | ML5 |
| 2 | 344 | 0.63 | 0.78 | 43 | empty |
| 3 | 82 | 0.61 | 0.88 | 17 | empty |
| 4 | 212 | 0.51 | 0.76 | 29 | empty |
| 5 | 107 | 0.33 | 0.72 | 21 | empty |
Modifications
Observed in the structure: 2 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3V2W · Crystal Structure of a Lipid G protein-Coupled Receptor at 3.35A · the same entry in another collection · chain A against A, TM-score 1.00
- P21453 · AlphaFold monomer V2.0 prediction for sphingosine 1-phosphate receptor 1 (P21453) · a predicted model of the same protein · chain A against A, TM-score 0.65
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 P21453
- Every structure of UniProt P00720
- Elsewhere: RCSB PDB 3V2W · PDBe 3V2W · UniProt P21453 · UniProt P00720
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